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Liu W, He X, Zhu Y, Li Y, Wang Z, Li P, Pan J, Wang J, Chu B, Yang G, Zhang M, He Q, Li Y, Li W, Zhang C. Identification of a conserved G-quadruplex within the E165R of African swine fever virus (ASFV) as a potential antiviral target. J Biol Chem 2024; 300:107453. [PMID: 38852886 DOI: 10.1016/j.jbc.2024.107453] [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: 11/29/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024] Open
Abstract
Identification of a conserved G-quadruplex in E165R of ASFVAfrican swine fever virus (ASFV) is a double-stranded DNA arbovirus with high transmissibility and mortality rates. It has caused immense economic losses to the global pig industry. Currently, no effective vaccines or medications are to combat ASFV infection. G-quadruplex (G4) structures have attracted increasing interest because of their regulatory role in vital biological processes. In this study, we identified a conserved G-rich sequence within the E165R gene of ASFV. Subsequently, using various methods, we verified that this sequence could fold into a parallel G4. In addition, the G4-stabilizers pyridostatin and 5,10,15,20-tetrakis-(N-methyl-4-pyridyl) porphin (TMPyP4) can bind and stabilize this G4 structure, thereby inhibiting E165R gene expression, and the inhibitory effect is associated with G4 formation. Moreover, the G4 ligand pyridostatin substantially impeded ASFV proliferation in Vero cells by reducing gene copy number and viral protein expression. These compelling findings suggest that G4 structures may represent a promising and novel antiviral target against ASFV.
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Affiliation(s)
- Wenhao Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Xinglin He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Yance Zhu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Yaqin Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Zhihao Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Pengfei Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Jiajia Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Beibei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Guoyu Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Mengjia Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Qigai He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Wentao Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
| | - Chao Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China.
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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Chan KH, Wang Y, Zheng BX, Long W, Feng X, Wong WL. RNA-Selective Small-Molecule Ligands: Recent Advances in Live-Cell Imaging and Drug Discovery. ChemMedChem 2023; 18:e202300271. [PMID: 37649155 DOI: 10.1002/cmdc.202300271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/13/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
RNA structures, including those formed from coding and noncoding RNAs, alternative to protein-based drug targets, could be a promising target of small molecules for drug discovery against various human diseases, particularly in anticancer, antibacterial and antivirus development. The normal cellular activity of cells is critically dependent on the function of various RNA molecules generated from DNA transcription. Moreover, many studies support that mRNA-targeting small molecules may regulate the synthesis of disease-related proteins via the non-covalent mRNA-ligand interactions that do not involve gene modification. RNA-ligand interaction is thus an attractive approach to address the challenge of "undruggable" proteins in drug discovery because the intracellular activity of these proteins is hard to be suppressed with small molecule ligands. We selectively surveyed a specific area of RNA structure-selective small molecule ligands in fluorescence live cell imaging and drug discovery because the area was currently underexplored. This state-of-the-art review thus mainly focuses on the research published within the past three years and aims to provide the most recent information on this research area; hopefully, it could be complementary to the previously reported reviews and give new insights into the future development on RNA-specific small molecule ligands for live cell imaging and drug discovery.
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Affiliation(s)
- Ka Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Yakun Wang
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Wei Long
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Xinxin Feng
- State Key Laboratory of Chem-/Bio-Sensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
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Sannikova NE, Kolokolov MI, Khlynova TA, Chubarov AS, Polienko YF, Fedin MV, Krumkacheva OA. Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study. Phys Chem Chem Phys 2023; 25:22455-22466. [PMID: 37581249 DOI: 10.1039/d3cp01775c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable importance in medicinal chemistry and drug discovery due to their promising potential in photodynamic therapy applications. G4s can experience structural changes as a result of ligand interactions and light exposure. Understanding these modifications is essential to uncover the fundamental biological roles of the complexes and optimize their therapeutic potential. The structural diversity of G4s makes it challenging to study their complexes with ligands, necessitating the use of various complementary methods to fully understand these interactions. In this study, we introduce, for the first time, the application of laser-induced dipolar EPR as a method to characterize G-quadruplex DNA complexes containing photosensitizers and to investigate light-induced structural modifications in these systems. To demonstrate the feasibility of this approach, we studied complexes of the human telomeric G-quadruplex (HTel-22) with cationic 5,10,15,20-tetrakis(1-methyl-4-pyridinio) porphyrin tetra(p-toluenesulfonate) (TMPyP4). In addition to showcasing a new methodology, we also aimed to provide insights into the mechanisms underlying photoinduced HTel-22/TMPyP4 structural changes, thereby aiding in the advancement of approaches targeting G4s in photodynamic therapy. EPR revealed G-quadruplex unfolding and dimer formation upon light exposure. Our findings demonstrate the potential of EPR spectroscopy for examining G4 complexes with photosensitizers and contribute to a better understanding of G4s' interactions with ligands under light.
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Affiliation(s)
- Natalya E Sannikova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Mikhail I Kolokolov
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Tamara A Khlynova
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Yuliya F Polienko
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
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Bag S, Ghosal S, Karmakar S, Pramanik G, Bhowmik S. Uncovering the Contrasting Binding Behavior of Plant Flavonoids Fisetin and Morin Having Subsidiary Hydroxyl Groups (-OH) with HRAS1 and HRAS2 i-Motif DNA Structures: Decoding the Structural Alterations and Positional Influences. ACS OMEGA 2023; 8:30315-30329. [PMID: 37636929 PMCID: PMC10448647 DOI: 10.1021/acsomega.3c03105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023]
Abstract
Research on the interactions of naturally existing flavonoids with various noncanonical DNA such as i-motif (IM) DNA structures is helpful in comprehending the molecular basis of binding mode as well as providing future direction for the application and invention of novel effective therapeutic drugs. IM DNA structures have been identified as prospective anticancer therapeutic targets, and flavonoids are smaller molecules with a variety of health-promoting attributes, including anticancer activities. The extensive investigation comprising a series of techniques reveals the contrasting mode of the binding behavior of fisetin and morin with various IM DNA structures. We have discovered that structural alterations of hydroxyl groups located at different places of aromatic rings influence flavonoid's reactivity. This minor structural alteration appears to be critical for fisetin and morin's capacity to interact differentially with HRAS1 and HRAS2 IM DNA. Hence, fisetin appears to be an efficient ligand for HRAS1 and morin is considered to be an efficient ligand for HRAS2 IM DNA. This novel exploration opens up the possibility of employing the strategy for regulation of gene expression in cancerous cells. Our finding also reveals the flavonoid-mediated specific interaction with IM DNA while pointing toward tangible strategies for drug discovery and other essential cellular functions.
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Affiliation(s)
- Sagar Bag
- Department
of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Souvik Ghosal
- Mahatma
Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth
(Deemed to be University), Pondy−Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
| | - Sudip Karmakar
- UGC−DAE
Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Goutam Pramanik
- UGC−DAE
Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Sudipta Bhowmik
- Department
of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
- Mahatma
Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth
(Deemed to be University), Pondy−Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
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