1
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Li D, Tian T, Ko CN, Yang C. Prospect of targeting lysine methyltransferase NSD3 for tumor therapy. Pharmacol Res 2023; 194:106839. [PMID: 37400043 DOI: 10.1016/j.phrs.2023.106839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/05/2023]
Abstract
Nuclear receptor binding SET domain protein 3 (NSD3) has recently been recognized as a new epigenetic target in the fight against cancer. NSD3, which is amplified, overexpressed or mutated in a variety of tumors, promotes tumor development by regulating the cell cycle, apoptosis, DNA repair and EMT. Therefore, the inhibition, silencing or knockdown of NSD3 are highly promising antitumor strategies. This paper summarizes the structure and biological functions of NSD3 with an emphasis on its carcinogenic or cancer-promoting activity. The development of NSD3-specific inhibitors or degraders is also discussed and reviewed in this paper.
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Affiliation(s)
- Dan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Tiantian Tian
- Center for Biological Science and Technology, Beijing Normal University, Zhuhai, Guangdong Province, 519087, China
| | - Chung-Nga Ko
- C-MER Dennis Lam and Partners Eye Center, Hong Kong International Eye Care Group, Hong Kong, China.
| | - Chao Yang
- National Engineering Research Center For Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, Zhejiang Province 316022, China.
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2
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Song YQ, Li GD, Niu D, Chen F, Jing S, Wai Wong VK, Wang W, Leung CH. A robust luminescent assay for screening alkyladenine DNA glycosylase inhibitors to overcome DNA repair and temozolomide drug resistance. J Pharm Anal 2023; 13:514-522. [PMID: 37305785 PMCID: PMC10257196 DOI: 10.1016/j.jpha.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/22/2023] [Accepted: 04/15/2023] [Indexed: 06/13/2023] Open
Abstract
Temozolomide (TMZ) is an anticancer agent used to treat glioblastoma, typically following radiation therapy and/or surgical resection. However, despite its effectiveness, at least 50% of patients do not respond to TMZ, which is associated with repair and/or tolerance of TMZ-induced DNA lesions. Studies have demonstrated that alkyladenine DNA glycosylase (AAG), an enzyme that triggers the base excision repair (BER) pathway by excising TMZ-induced N3-methyladenine (3meA) and N7-methylguanine lesions, is overexpressed in glioblastoma tissues compared to normal tissues. Therefore, it is essential to develop a rapid and efficient screening method for AAG inhibitors to overcome TMZ resistance in glioblastomas. Herein, we report a robust time-resolved photoluminescence platform for identifying AAG inhibitors with improved sensitivity compared to conventional steady-state spectroscopic methods. As a proof-of-concept, this assay was used to screen 1440 food and drug administration-approved drugs against AAG, resulting in the repurposing of sunitinib as a potential AAG inhibitor. Sunitinib restored glioblastoma (GBM) cancer cell sensitivity to TMZ, inhibited GBM cell proliferation and stem cell characteristics, and induced GBM cell cycle arrest. Overall, this strategy offers a new method for the rapid identification of small-molecule inhibitors of BER enzyme activities that can prevent false negatives due to a fluorescent background.
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Affiliation(s)
- Ying-Qi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Guo-Dong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Dou Niu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Shaozhen Jing
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, 999078, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao, 999078, China
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3
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Sadiq Z, Safiabadi Tali SH, Hajimiri H, Al-Kassawneh M, Jahanshahi-Anbuhi S. Gold Nanoparticles-Based Colorimetric Assays for Environmental Monitoring and Food Safety Evaluation. Crit Rev Anal Chem 2023:1-36. [PMID: 36629748 DOI: 10.1080/10408347.2022.2162331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Recent years have witnessed an exponential increase in the research on gold nanoparticles (AuNPs)-based colorimetric sensors to revolutionize point-of-use sensing devices. Hence, this review is compiled focused on current progress in the design and performance parameters of AuNPs-based sensors. The review begins with the characteristics of AuNPs, followed by a brief explanation of synthesis and functionalization methods. Then, the mechanisms of AuNPs-based sensors are comprehensively explained in two broad categories based on the surface plasmon resonance (SPR) characteristics of AuNPs and their peroxidase-like catalytic properties (nanozyme). SPR-based colorimetric sensors further categorize into aggregation, anti-aggregation, etching, growth-mediated, and accumulation-based methods depending on their sensing mechanisms. On the other hand, peroxidase activity-based colorimetric sensors are divided into two methods based on the expression or inhibition of peroxidase-like activity. Next, the analytes in environmental and food samples are classified as inorganic, organic, and biological pollutants, and recent progress in detection of these analytes are reviewed in detail. Finally, conclusions are provided, and future directions are highlighted. Improving the sensitivity, reproducibility, multiplexing capabilities, and cost-effectiveness for colorimetric detection of various analytes in environment and food matrices will have significant impact on fast testing of hazardous substances, hence reducing the pollution load in environment as well as rendering food contamination to ensure food safety.
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Affiliation(s)
- Zubi Sadiq
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering and Computer Science, Concordia University, Montréal, Québec, Canada
| | - Seyed Hamid Safiabadi Tali
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering and Computer Science, Concordia University, Montréal, Québec, Canada
| | - Hasti Hajimiri
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering and Computer Science, Concordia University, Montréal, Québec, Canada
| | - Muna Al-Kassawneh
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering and Computer Science, Concordia University, Montréal, Québec, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering and Computer Science, Concordia University, Montréal, Québec, Canada
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4
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Yang GJ, Li D, Ko CN, Guo S, Yang C. Editorial: Immunomodulatory role of metalloproteases in chronic inflammatory diseases. Front Immunol 2023; 14:1196791. [PMID: 37114053 PMCID: PMC10126522 DOI: 10.3389/fimmu.2023.1196791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- *Correspondence: Guan-Jun Yang, ; Shicheng Guo, ; Chung Nga Ko, ; Dan Li, ; Chao Yang,
| | - Dan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Guan-Jun Yang, ; Shicheng Guo, ; Chung Nga Ko, ; Dan Li, ; Chao Yang,
| | - Chung Nga Ko
- C−MER Dennis Lam and Partners Eye Center, Hong Kong International Eye Care Group, Hong Kong, Hong Kong SAR, China
- *Correspondence: Guan-Jun Yang, ; Shicheng Guo, ; Chung Nga Ko, ; Dan Li, ; Chao Yang,
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Guan-Jun Yang, ; Shicheng Guo, ; Chung Nga Ko, ; Dan Li, ; Chao Yang,
| | - Chao Yang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, China
- *Correspondence: Guan-Jun Yang, ; Shicheng Guo, ; Chung Nga Ko, ; Dan Li, ; Chao Yang,
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5
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Onaş AM, Dascălu C, Raicopol MD, Pilan L. Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets. BIOSENSORS 2022; 12:816. [PMID: 36290952 PMCID: PMC9599214 DOI: 10.3390/bios12100816] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.
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Affiliation(s)
- Andra Mihaela Onaş
- Advanced Polymer Materials Group, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Constanţa Dascălu
- Faculty of Applied Sciences, University ‘Politehnica’ of Bucharest, 313 Splaiul Independenţei, District 6, 060042 Bucharest, Romania
| | - Matei D. Raicopol
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Luisa Pilan
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
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Thapa S, Singh KRB, Verma R, Singh J, Singh RP. State-of-the-Art Smart and Intelligent Nanobiosensors for SARS-CoV-2 Diagnosis. BIOSENSORS 2022; 12:bios12080637. [PMID: 36005033 PMCID: PMC9405813 DOI: 10.3390/bios12080637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/16/2022]
Abstract
The novel coronavirus appeared to be a milder infection initially, but the unexpected outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), commonly called COVID-19, was transmitted all over the world in late 2019 and caused a pandemic. Human health has been disastrously affected by SARS-CoV-2, which is still evolving and causing more serious concerns, leading to the innumerable loss of lives. Thus, this review provides an outline of SARS-CoV-2, of the traditional tools to diagnose SARS-CoV-2, and of the role of emerging nanomaterials with unique properties for fabricating biosensor devices to diagnose SARS-CoV-2. Smart and intelligent nanomaterial-enabled biosensors (nanobiosensors) have already proven their utility for the diagnosis of several viral infections, as various detection strategies based on nanobiosensor devices are already present, and several other methods are also being investigated by researchers for the determination of SARS-CoV-2 disease; however, considerably more is undetermined and yet to be explored. Hence, this review highlights the utility of various nanobiosensor devices for SARS-CoV-2 determination. Further, it also emphasizes the future outlook of nanobiosensing technologies for SARS-CoV-2 diagnosis.
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Affiliation(s)
- Sushma Thapa
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Kshitij RB Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ranjana Verma
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Jay Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
- Correspondence: (J.S.); or (R.P.S.)
| | - Ravindra Pratap Singh
- Department of Biotechnology, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak 484887, Madhya Pradesh, India
- Correspondence: (J.S.); or (R.P.S.)
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7
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Development of Fluorescent Aptasensors Based on G-Quadruplex Quenching Ability for Ochratoxin A and Potassium Ions Detection. BIOSENSORS 2022; 12:bios12060423. [PMID: 35735570 PMCID: PMC9221108 DOI: 10.3390/bios12060423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022]
Abstract
G-quadruplexes have received significant attention in aptasensing due to their structural polymorphisms and unique binding properties. In this work, we exploited the fluorescence-quenching properties of G-quadruplex to develop a simple, fast, and sensitive platform for fluorescence detection of ochratoxin A (OTA) and potassium ions (K+) with a label-free fluorophore and quencher strategy. The quenching ability of G-quadruplex was confirmed during the recognition process after the formation of the G-quadruplex structure and the quenching of the labeled fluorescein fluorophore (FAM). The fluorescence-quenching mechanism was studied by introducing specific ligands of G-quadruplex to enhance the quenching effect, to show that this phenomenon is due to photo-induced electron transfer. The proposed fluorescence sensor based on G-quadruplex quenching showed excellent selectivity with a low detection limit of 0.19 nM and 0.24 µM for OTA and K+, respectively. Moreover, we demonstrated that our detection method enables accurate concentration determination of real samples with the prospect of practical application. Therefore, G-quadruplexes can be excellent candidates as quenchers, and the strategy implemented in the study can be extended to an aptasensor with G-quadruplex.
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8
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Qi P, Yi M, Song A, Hao J. Guanine Analogue-Based Assemblies: Construction and Luminescence Functions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7099-7106. [PMID: 35648843 DOI: 10.1021/acs.langmuir.2c00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As one of the natural nucleobases, guanine has attracted increasing interest in molecular self-assembly science because of its abundant interaction sites and high electron cloud density. Guanines, guanine derivatives, and guanine-rich DNA sequence are able to self-assemble into versatile aggregate structures by the means of hydrogen bonds and π-π, ion-dipole, solvophobic, and electrostatic interactions. Recent advances have shown that many guanine analogue-based (G-based) luminescent aggregates exhibit promising applications for fluorescent and chemiluminescent sensing and circularly polarized luminescence (CPL). This perspective summarizes the state-of-art strategies for constructing G-based assemblies and presents representative examples for luminescence functions. Finally, the inspirations are provided for exploiting unique G-based systems and luminescent G-based assemblies.
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Affiliation(s)
- Ping Qi
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Mengjiao Yi
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Aixin Song
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan 250100, China
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9
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Ratiometric detection of transcription factor based on Europium(III) complex-doped silicon nanoparticles and a G-quadruplex-selective Iridium(III) complex. Anal Chim Acta 2022; 1209:339855. [DOI: 10.1016/j.aca.2022.339855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022]
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10
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Chen F, Li G, Wu C, Wang L, Ko CN, Ma DL, Leung CH. Interference Reduction Biosensing Strategy for Highly Sensitive microRNA Detection. Anal Chem 2022; 94:4513-4521. [PMID: 35234447 DOI: 10.1021/acs.analchem.2c00138] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
MicroRNAs are potential biomarkers for human cancers and other diseases due to their roles as post-transcriptional regulators for gene expression. However, the detection of miRNAs by conventional methods such as RT-qPCR, in situ hybridization, northern blot-based platforms, and next-generation sequencing is complicated by short length, low abundance, high sequence homology, and susceptibility to degradation of miRNAs. In this study, we developed a nicking endonuclease-mediated interference reduction rolling circle amplification (NEM-IR-RCA) strategy for the ultrasensitive and highly specific detection of miRNA-21. This method exploits the advantages of the optical properties of long-lived iridium(III) probes, in conjunction with time-resolved emission spectroscopy (TRES) and exponential rolling circle amplification (E-RCA). Under the NEM-IR-RCA-based signal enhancement processes, the limit of detection of miRNA-21 was down to 0.0095 fM with a linear range from 0.05 to 100 fM, which is comparable with the conventional RT-qPCR. Unlike RT-qPCR, the strategy was performed at a lower and constant temperature without heating/cooling cycles and reverse transcription. The strategy could clearly discriminate between matched and mismatched targets, demonstrating high specificity. Moreover, the potential application of this method was demonstrated in cancer cells and mouse serum samples, showing good agreement with RT-qPCR results. Apart from miRNA-21 detection, this platform could be also adapted for detecting other miRNAs, such as let-7a and miRNA-22, indicating its excellent potential for biomedical research and clinical diagnostics.
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Affiliation(s)
- Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China.,Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Ling Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Chung-Nga Ko
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, China.,Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China.,Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
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11
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Chen F, Li G, Wu C, Wang W, Ma DL, Leung CH. A rapid and label-free DNA-based interference reduction nucleic acid amplification strategy for viral RNA detection. Biosens Bioelectron 2022; 198:113829. [PMID: 34840016 DOI: 10.1016/j.bios.2021.113829] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/11/2021] [Accepted: 11/19/2021] [Indexed: 12/26/2022]
Abstract
Common reference methods for COVID-19 diagnosis include thermal cycling amplification (e.g. RT-PCR) and isothermal amplification methods (e.g. LAMP and RPA). However, they may not be suitable for direct detection in environmental and biological samples due to background signal interference. Here, we report a rapid and label-free interference reduction nucleic acid amplification strategy (IR-NAAS) that exploits the advantages of luminescent iridium(III) probes, time-resolved emission spectroscopy (TRES) and multi-branch rolling circle amplification (mbRCA). Using IR-NAAS, we established a luminescence approach for diagnosing COVID-19 RNAs sequences RdRp, ORF1ab and N with a linear range of 0.06-6.0 × 105 copies/mL and a detection limit of down to 7.3 × 104 copies/mL. Moreover, the developed method was successfully applied to detect COVID-19 RNA sequences from various environmental and biological samples, such as domestic sewage, and mice urine, blood, feces, lung tissue, throat and nasal secretions. Apart from COVID-19 diagnosis, IR-NAAS was also demonstrated for detecting other RNA viruses, such as H1N1 and CVA10, indicating that this approach has great potential approach for routine preliminary viral detection.
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Affiliation(s)
- Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China; Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China.
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12
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Li G, Liu H, Feng R, Kang TS, Wang W, Ko CN, Wong CY, Ye M, Ma DL, Wan JB, Leung CH. A bioactive ligand-conjugated iridium(III) metal-based complex as a Keap1-Nrf2 protein-protein interaction inhibitor against acetaminophen-induced acute liver injury. Redox Biol 2021; 48:102129. [PMID: 34526248 PMCID: PMC8710994 DOI: 10.1016/j.redox.2021.102129] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 01/04/2023] Open
Abstract
Hepatotoxicity caused by an overdose of acetaminophen (APAP) is the leading reason for acute drug-related liver failure. Nuclear factor erythroid-2-related factor 2 (Nrf2) is a protein that helps to regulate redox homeostasis and coordinate stress responses via binding to the Kelch-like ECH-associated protein 1 (Keap1). Targeting the Keap1-Nrf2 interaction has recently emerged as a potential strategy to alleviate liver injury caused by APAP. Here, we designed and synthesized a number of iridium (III) and rhodium (III) complexes bearing ligands with reported activity against oxidative stress, which is associated with Nrf2 transcriptional activation. The iridium (III) complex 1 bearing a bioactive ligand 2,9-dimethyl-1,10-phenanthroline and 4-chloro-2-phenylquinoline, a derivative of the bioactive ligand 2-phenylquinoline, was identified as a direct small-molecule inhibitor of the Keap1–Nrf2 protein-protein interaction. 1 could stabilize Keap1 protein, upregulate HO-1 and NQO1, and promote Nrf2 nuclear translocation in normal liver cells. Moreover, 1 reversed APAP-induced liver damage by disrupting Keap1–Nrf2 interaction and without inducing organ damage and immunotoxicity in mice. Our study demonstrates the identification of a selective and efficacious antagonist of Keap1–Nrf2 interaction possessed good cellular permeability in cellulo and ideal pharmacokinetic parameters in vivo, and, more importantly, validates the feasibility of conjugating metal complexes with bioactive ligands to generate metal-based drug leads as non-toxic Keap1–Nrf2 interaction inhibitors for treating APAP-induced acute liver injury. 1 reversed APAP-induced liver damage by disrupting Keap1–Nrf2 interaction without inducing organ damage or immunotoxicity. Complex 1 possessed good cellular permeability in cellulo and ideal pharmacokinetic parameters in vivo. Conjugating metal complexes with bioactive ligands opens a novel avenue for the treatment of APAP-induced liver damage.
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Affiliation(s)
- Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
| | - Hao Liu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Ruibing Feng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China; Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Chung-Nga Ko
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yuen Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong SAR, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China.
| | - Jian-Bo Wan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, China.
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13
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Walia S, Chandrasekaran AR, Chakraborty B, Bhatia D. Aptamer-Programmed DNA Nanodevices for Advanced, Targeted Cancer Theranostics. ACS APPLIED BIO MATERIALS 2021; 4:5392-5404. [PMID: 35006722 DOI: 10.1021/acsabm.1c00413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA has been demonstrated to be a versatile material for construction at the nanoscale. DNA nanodevices are highly programmable and allow functionalization with multiple entities such as imaging modalities (fluorophores), targeting entities (aptamers), drug conjugation (chemical linkers), and triggered release (photoresponsive molecules). These features enhance the use of DNA nanodevices in biological applications, catalyzing the rapid growth of this domain of research. In this review, we focus on recent progress in the development and use of aptamer-functionalized DNA nanodevices as theranostic agents, their characterization, applications as delivery platforms, and advantages. We provide a brief background on the development of aptamers and DNA nanodevices in biomedical applications, and we present specific applications of these entities in cancer diagnosis and therapeutics. We conclude with a perspective on the challenges and possible solutions for the clinical translation of aptamer-functionalized DNA nanodevices in the domain of cancer therapeutics.
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Affiliation(s)
- Shanka Walia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | | | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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14
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Pirota V, Platella C, Musumeci D, Benassi A, Amato J, Pagano B, Colombo G, Freccero M, Doria F, Montesarchio D. On the binding of naphthalene diimides to a human telomeric G-quadruplex multimer model. Int J Biol Macromol 2020; 166:1320-1334. [PMID: 33166559 DOI: 10.1016/j.ijbiomac.2020.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
To selectively target telomeric G-quadruplex (G4) DNA, monomeric and dimeric naphthalene diimides (NDIs) were investigated as binders of multimeric G4 structures able to discriminate duplex DNA. These NDIs were analysed by the affinity chromatography-based screening G4-CPG (G-quadruplex on Controlled Pore Glass), using the sequence d[AGGG(TTAGGG)7] (tel46), folding into two consecutive G4s, as model of the human telomeric G4 multimer. In parallel, a telomeric G4 monomer (tel26) and a duplex structure (ds27) were used as controls. According to G4-CPG screening, NDI-5 proved to be the best ligand in terms of dimeric G4 vs. duplex DNA selectivity and was analysed by circular dichroism (CD), gel electrophoresis, isothermal titration calorimetry (ITC) and fluorescence spectroscopy in its interactions with tel46. NDI-5 strongly binds and stabilizes tel46 G4, favouring a hybrid folding in K+-containing buffer. Under these conditions, the binding process comprises a first event involving three molecules of NDI-5 and a second one in which other six molecules bind to the DNA. In a metal cation-free system, NDI-5 induces tel46 G4 folding, as indicated by CD and PAGE, favouring an antiparallel structuring. Docking simulations showed that NDI-5 can effectively bind to the pocket between two G4 units, representing a promising ligand for multimeric G4s.
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Affiliation(s)
- Valentina Pirota
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
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15
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Xi H, Juhas M, Zhang Y. G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection. Biosens Bioelectron 2020; 167:112494. [PMID: 32791468 PMCID: PMC7403137 DOI: 10.1016/j.bios.2020.112494] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/26/2020] [Accepted: 07/31/2020] [Indexed: 12/29/2022]
Abstract
G-quadruplex is a non-canonical nucleic acid structure formed by the folding of guanine rich DNA or RNA. The conformation and function of G-quadruplex are determined by a number of factors, including the number and polarity of nucleotide strands, the type of cations and the binding targets. Recent studies led to the discovery of additional advantageous attributes of G-quadruplex with the potential to be used in novel biosensors, such as improved ligand binding and unique folding properties. G-quadruplex based biosensor can detect various substances, such as metal ions, organic macromolecules, proteins and nucleic acids with improved affinity and specificity compared to standard biosensors. The recently developed G-quadruplex based biosensors include electrochemical and optical biosensors. A novel G-quadruplex based biosensors also show better performance and broader applications in the detection of a wide spectrum of pathogens, including SARS-CoV-2, the causative agent of COVID-19 disease. This review highlights the latest developments in the field of G-quadruplex based biosensors, with particular focus on the G-quadruplex sequences and recent applications and the potential of G-quadruplex based biosensors in SARS-CoV-2 detection.
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Affiliation(s)
- Hui Xi
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China.
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16
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Nao SC, Wu KJ, Wang W, Leung CH, Ma DL. Recent Progress and Development of G-Quadruplex-Based Luminescent Assays for Ochratoxin A Detection. Front Chem 2020; 8:767. [PMID: 33088800 PMCID: PMC7490745 DOI: 10.3389/fchem.2020.00767] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Ochratoxin A (OTA) is a mycotoxin that is widespread throughout the world. It contaminates foods such as vegetables, fruits, and rice. It harms human health and has potential carcinogenic effects. The G-quadruplex (G4) is a tetraplexed DNA structure generated from guanine-rich DNA that has found emerging use in aptamer-based sensing systems. This review outlines the status of OTA contamination and conventional detection methods for OTA. Various G4-based methods to detect OTA developed in recent years are summarized along with their advantages and disadvantages compared to existing approaches.
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Affiliation(s)
- Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Ke-Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Wanhe Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, China
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17
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Hong CY, Zhang XX, Dai CY, Wu CY, Huang ZY. Highly sensitive detection of multiple antibiotics based on DNA tetrahedron nanostructure-functionalized magnetic beads. Anal Chim Acta 2020; 1120:50-58. [PMID: 32475391 DOI: 10.1016/j.aca.2020.04.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 01/03/2023]
Abstract
Functional DNAs-functionalized magnetic beads (MBs) offer great potential in bioanalysis field because of their target recognition and magnetic separation functions. However, the recognition capability and hybridization affinity of DNA probes often suffer from limited available space, poor probe conformation and non-selective adsorption. To overcome these limitations, we herein used aptamer-pendant DNA tetrahedron nanostructure-functionalized MBs (TETapt-tet MBs) to develop a target-response fluorescence method with tetracycline (TET) as a model. In the absence of TET, 6-carboxy-X-rhodamine-labeled complementary DNAs (ROX-cDNAs) were assembled on the surface of MBs. Upon the addition of target TET, the ROX-cDNAs were separated and released from the MBs to generate fluorescence signal. The limit of detection and limit of quantification for TET were found to be 6 pg mL-1 and 20 pg mL-1, respectively. Compared with ssDNA-functionalized MBs surface, the designed DNA tetrahedron nanostructure-based surface could decrease the hybridization time and reduce false positives, ensuring the accuracy of TET detection in complex samples. The presented method was successfully employed for TET detection in honey samples. Moreover, this functionalization strategy could be extended to detect multiple antibiotics by simply substituting different aptamer sequences. Therefore, the proposed method has great potential in the field of food safety and public health.
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Affiliation(s)
- Cheng-Yi Hong
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
| | - Xiao-Xia Zhang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Chen-Ying Dai
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Chen-Yue Wu
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zhi-Yong Huang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021, China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, 361021, China.
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18
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Lo KKW. Molecular Design of Bioorthogonal Probes and Imaging Reagents Derived from Photofunctional Transition Metal Complexes. Acc Chem Res 2020; 53:32-44. [PMID: 31916746 DOI: 10.1021/acs.accounts.9b00416] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For more than 15 years, bioorthogonal chemistry has received increasing attention due to its successful applications in the detection and imaging of biomolecules in their native biological environments. The method typically proceeds with the incorporation of a biological substrate appended with a bioorthogonal functional group (chemical reporter), followed by the introduction of the substrate to biological systems. Biomolecules containing the substrate are then recognized by an exogenously delivered bioorthogonal probe. Despite the fact that many useful chemical reporters and bioorthogonal reactions have been developed, most of the bioorthogonal probes reported thus far are fluorescent dyes. A limitation is that stringent washing is required due to the interference caused by the background fluorescence of unreacted probes. Thus, fluorogenic probes with turn-on emission properties upon bioorthogonal labeling have been designed as an alternative strategy. These probes are highly appealing because excellent images can be obtained without the need for washing steps. Nearly all fluorogenic bioorthogonal probes designed are essentially organic dyes, their emission is limited to fluorescence, and the utilization of the probes is confined to bioimaging applications. Recently, there has been a growing interest in the bioimaging and therapeutic applications of luminescent inorganic and organometallic transition metal complexes due to their intriguing photophysical and photochemical properties, high membrane permeability, controllable cellular uptake, intracellular localization, and cytotoxicity. We anticipate that photofunctional transition metal complexes can be exploited as valuable bioorthogonal probes due to these appealing advantages. In this Account, we introduce the molecular design, photophysical and photochemical properties, and biological applications of various bioorthogonal probes and imaging reagents based on photofunctional transition metal complexes. The presence of a cationic metal center significantly enhances the bioorthogonal reactivity of the probes, yet their stability in aqueous solutions can be maintained. Interestingly, some of these metal complexes are strategically modified to display phosphorogenic properties, that is, phosphorescence turn-on upon bioorthogonal labeling reactions. Importantly, these probes not only exhibit favorable photophysical properties after bioorthogonal labeling, but also efficient photoinduced singlet oxygen (1O2) generation. This interesting bioorthogonal reaction-triggered photosensitization capability allows the modulation of 1O2 generation efficiency and contributes to the development of controllable photocytotoxic agents. The exploration of transition metal complex-based probes not only significantly widens the scope of bioorthogonal labeling but also further highlights the unique advantages of these complexes in the design of theranostic reagents. The development of these innovative reagents is expected to contribute to the basic understanding of biological processes in living systems and provide exciting opportunities for new diagnostic and therapeutic applications.
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Affiliation(s)
- Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, P. R. China
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19
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Yang H, Zhao W, Deng S, Zhang K, Zhao Z, Deng R, He Q, Li J. Intrinsic Conformation-Induced Fluorescence Resonance Energy Transfer Aptasensor. ACS APPLIED BIO MATERIALS 2019; 3:2553-2559. [DOI: 10.1021/acsabm.9b00738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Wenyue Zhao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhifeng Zhao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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20
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Raje S, Barthwal R. Molecular recognition of 3+1 hybrid human telomeric G-quadruplex DNA d-[AGGG(TTAGGG) 3] by anticancer drugs epirubicin and adriamycin leads to thermal stabilization. Int J Biol Macromol 2019; 139:1272-1287. [PMID: 31421170 DOI: 10.1016/j.ijbiomac.2019.08.109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 11/30/2022]
Abstract
Recent reports suggest influence of anti-cancer anthracyclines on telomere dysfunction and their possible interaction with G-quadruplex (G4) DNA as an alternate pathway to apoptosis. We have investigated interaction of epirubicin and adriamycin with G4 DNA [d-AGGG(TTAGGG)3] comprising human telomeric DNA sequence by surface plasmon resonance, absorption, fluorescence, circular dichroism and thermal denaturation. Epirubicin and adriamycin bind with affinity, Kb, = 2.5×105 and 5.2×105M-1, respectively in monomeric form leading to decrease in absorbance, fluorescence quenching and ellipticity changes without any significant shift in absorption emission maxima with corresponding induced thermal stabilization by 13.0 and 11.6°C in K+ rich solution. Na+ ions did not induce any thermal stabilization. Molecular docking confirmed external binding at grooves and loops of G4 DNA involving 4OCH3 of ring D, 9COCH2OH of ring A, 4'OH/H and 3'NH3+ of daunosamine sugar. Thermal stabilization induced by specific interactions is likely to hamper telomere association with telomerase enzyme and contribute to drug-induced apoptosis in cancer cell lines besides causing damage to duplex DNA. The findings pave the way for drug designing in view of immense possibilities of altering substituent groups on anthracyclines for enhancement of efficacy, reduced cell toxicity as well as specificity towards G-quadruplex DNA.
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Affiliation(s)
- Shailja Raje
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ritu Barthwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India.
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21
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Abstract
G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only ~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5'- and 3'-untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure.
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Affiliation(s)
- Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, IN USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN USA
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22
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Si MK, Pramanik SK, Ganguly B. Tuning the ring strain effect in acridine derivatives on binding affinity with G-quadruplex-DNA: A computational and experimental study. Int J Biol Macromol 2018; 124:1177-1185. [PMID: 30521912 DOI: 10.1016/j.ijbiomac.2018.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 12/01/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
Search for inhibitors to stabilize the telomeric G-quadruplex in order to deter telomerase activity is an active area of research. Inhibitors play an important role to initiate the tumor cell mortalization process. This work reports for the first time of acridine derivative with four membered ammonium rings at the side chain to surpass the binding ability against BRACO-19 with G-quadruplex-DNA. It is known in the literature that acridine based molecule BRACO-19 can effectively bind with G-quadruplex-DNA. The computational study performed in this study revealed that the binding ability of acridine based molecule can be augmented with subtle variation in the molecular structure of the drug like candidates. Steered molecular dynamics (SMD) performed with the acridine derivatives and G-quadruplex DNA showed the importance of ring strain to the side chain of those ligand molecules. The rupture force analysis, hydrogen bonding interactions and the calculated free energies in MM-PBSA method suggest that ligand 3 is superior than that of BRACO-19. The synthesized ligand 3 and BRACO-19 showed the binding constants obtained from ITC measurements are 4 × 106 mol-1 and 2.6 × 106, which corroborates the computational findings.
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Affiliation(s)
- Mrinal Kanti Si
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, India; Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat 364 002, India
| | - Sumit Kumar Pramanik
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, India; Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat 364 002, India.
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23
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Tariq Z, Barthwal R. Binding of anticancer drug daunomycin to parallel G-quadruplex DNA [d-(TTGGGGT)]4 leads to thermal stabilization: A multispectroscopic investigation. Int J Biol Macromol 2018; 120:1965-1974. [DOI: 10.1016/j.ijbiomac.2018.09.154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
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24
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Evangelista BA, Kim YS, Kolpashchikov DM. FaptaSyme: A Strategy for Converting a Monomer/Oligomer-Nonselective Aptameric Sensor into an Oligomer-Selective One. Chembiochem 2018; 19:10.1002/cbic.201800017. [PMID: 29700982 PMCID: PMC6422747 DOI: 10.1002/cbic.201800017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 12/26/2022]
Abstract
Aptameric sensors can bind molecular targets and produce output signals, a phenomenon that is used in bioassays. In some cases, it is important to distinguish between monomeric and oligomeric forms of a target. Here, we propose a strategy to convert a monomer/oligomer-nonselective sensor into an oligomer-selective sensor. We designed an aptazyme that produced a high fluorescent output in the presence of oligomeric α-synuclein (a molecular marker of Parkinson's disease) but not its monomeric form. The strategy is potentially useful in the design of point-of-care tests for the diagnosis of neurodegenerative diseases.
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Affiliation(s)
- Baggio A. Evangelista
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA
| | - Yoon-Seong Kim
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA
| | - Dmitry M. Kolpashchikov
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA,
- ITMO University, Laboratory of Solution Chemistry of Advanced Materials and Technologies, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation
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25
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Ma Y, Tsushima Y, Sakuma M, Sasaki S, Iida K, Okabe S, Seimiya H, Hirokawa T, Nagasawa K. Development of G-quadruplex ligands for selective induction of a parallel-type topology. Org Biomol Chem 2018; 16:7375-7382. [DOI: 10.1039/c8ob01702f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Parallel type of topology in G4 is selectively induced by tetra-guanidinylalkyl substituted 6OTD derivative.
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Affiliation(s)
- Yue Ma
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Yamato Tsushima
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Mai Sakuma
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Shogo Sasaki
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Keisuke Iida
- Department of Chemistry
- Faculty of Science
- Chiba University
- Chiba 263-8522
- Japan
| | - Sachiko Okabe
- Division of Molecular Biotherapy
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research
- Koto-ward
- Tokyo 135-8550
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research
- Koto-ward
- Tokyo 135-8550
| | - Takatsugu Hirokawa
- Transborder Medical Research Center
- University of Tsukuba
- Tsukuba, 305-8575
- Japan
- Division of Biomedical Science
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
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