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Deb A, Nagpal S, Yadav RK, Thakur H, Nair D, Krishnan V, Vrati S. Japanese encephalitis virus NS5 protein interacts with nucleolin to enhance the virus replication. J Virol 2024:e0085824. [PMID: 39078257 DOI: 10.1128/jvi.00858-24] [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: 05/16/2024] [Accepted: 06/29/2024] [Indexed: 07/31/2024] Open
Abstract
Japanese encephalitis virus (JEV) is an arthropod-borne, plus-strand flavivirus causing viral encephalitis in humans with a high case fatality rate. The JEV non-structural protein 5 (NS5) with the RNA-dependent RNA polymerase activity interacts with the viral and host proteins to constitute the replication complex. We have identified the multifunctional protein Nucleolin (NCL) as one of the several NS5-interacting host proteins. We demonstrate the interaction and colocalization of JEV NS5 with NCL in the virus-infected HeLa cells. The siRNA-mediated knockdown of NCL indicated that it was required for efficient viral replication. Importantly, JEV grew to higher titers in cells over-expressing exogenous NCL, demonstrating its pro-viral role. We demonstrated that NS5 interacted with the RRM and GAR domains of NCL. We show that the NCL-binding aptamer AS1411 containing the G-quadruplex (GQ) structure and the GQ ligand BRACO-19 caused significant inhibition of JEV replication. The antiviral effect of AS1411 and BRACO-19 could be overcome in HeLa cells by the overexpression of exogenous NCL. We demonstrated that the synthetic RNAs derived from the 3'-NCR of JEV genomic RNA containing the GQ sequence could bind NCL in vitro. The replication complex binding to the 3'-NCR is required for the viral RNA synthesis. It is likely that NCL present in the replication complex destabilizes the GQ structures in the genomic RNA, thus facilitating the movement of the replication complex resulting in efficient virus replication.IMPORTANCEJapanese encephalitis virus (JEV) is endemic in most parts of South-East Asia and the Western Pacific region, causing epidemics of encephalitis with a high case fatality rate. While a tissue culture-derived JEV vaccine is available, no antiviral therapy exists. The JEV NS5 protein has RNA-dependent RNA polymerase activity. Together with several host and viral proteins, it constitutes the replication complex necessary for virus replication. Understanding the interaction of NS5 with the host proteins could help design novel antivirals. We identified Nucleolin (NCL) as a crucial host protein interactor of JEV NS5 having a pro-viral role in virus replication. The NS5-interacting NCL binds to the G-quadruplex (GQ) structure sequence in the 3'-NCR of JEV RNA. This may smoothen the movement of the replication complex along the genomic RNA, thereby facilitating the virus replication. This study is the first report on how NCL, a host protein, helps in JEV replication through GQ-binding.
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Affiliation(s)
- Arundhati Deb
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Shilpi Nagpal
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Rajnesh Kumari Yadav
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Harsh Thakur
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Deepak Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Vengadesan Krishnan
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
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Fang P, Xie C, Pan T, Cheng T, Chen W, Xia S, Ding T, Fang J, Zhou Y, Fang L, Wei D, Xiao S. Unfolding of an RNA G-quadruplex motif in the negative strand genome of porcine reproductive and respiratory syndrome virus by host and viral helicases to promote viral replication. Nucleic Acids Res 2023; 51:10752-10767. [PMID: 37739415 PMCID: PMC10602871 DOI: 10.1093/nar/gkad759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
G-quadruplex (G4) is a unique secondary structure formed by guanine-rich nucleic acid sequences. Growing studies reported that the genomes of some viruses harbor G4 structures associated with viral replication, opening up a new field to dissect viral infection. Porcine reproductive and respiratory syndrome virus (PRRSV), a representative member of Arteriviridae, is an economically significant pathogen that has devastated the swine industry worldwide for over 30 years. In this study, we identified a highly conserved G-rich sequence with parallel-type G4 structure (named PRRSV-G4) in the negative strand genome RNA of PRRSV. Pyridostatin (PDS), a well-known G4-binding ligand, stabilized the PRRSV-G4 structure and inhibited viral replication. By screening the proteins interacting with PRRSV-G4 in PRRSV-infected cells and single-molecule magnetic tweezers analysis, we found that two helicases, host DDX18 and viral nsp10, interact with and efficiently unwound the PRRSV-G4 structure, thereby facilitating viral replication. Using a PRRSV reverse genetics system, we confirmed that recombinant PRRSV with a G4-disruptive mutation exhibited resistance to PDS treatment, thereby displaying higher replication than wild-type PRRSV. Collectively, these results demonstrate that the PRRSV-G4 structure plays a crucial regulatory role in viral replication, and targeting this structure represents a promising strategy for antiviral therapies.
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Affiliation(s)
- Puxian Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Congbao Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ting Pan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Ting Cheng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Sijin Xia
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Tong Ding
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Junkang Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanrong Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Dengguo Wei
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
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Ruggiero E, Richter SN. Targeting G-quadruplexes to achieve antiviral activity. Bioorg Med Chem Lett 2023; 79:129085. [PMID: 36423824 PMCID: PMC9760570 DOI: 10.1016/j.bmcl.2022.129085] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
With the emergence of new viruses in the human population and the fast mutation rates of existing viruses, new antiviral targets and compounds are needed. Most existing antiviral drugs are active against proteins of a handful of viruses. Most of these proteins in the end affect viral nucleic acid processing, but direct nucleic acid targeting is less represented due to the difficulty of selectively acting at the nucleic acid of interest. Recently, nucleic acids have been shown to fold in structures alternative to the classic double helix and Watson and Crick base-pairing. Among these non-canonical structures, G-quadruplexes (G4s) have attracted interest because of their key biological roles that are being discovered. Molecules able to selectively target G4s have been developed and since G4s have been investigated as targets in several human pathologies, including viral infections. Here, after briefly introducing viruses, G4s and the G4-binding molecules with antiviral properties, we comment on the mechanisms at the base of the antiviral activity reported for G4-binding molecules. Understanding how G4-ligands act in infected cells will possibly help designing and developing next-generation antiviral drugs.
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Affiliation(s)
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Italy; Microbiology and Virology Unit, Padua University Hospital, Padua, Italy.
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Lv L, Zhang L. G-quadruplexes in the monkeypox virus are potential antiviral targets. J Med Virol 2023; 95:e28299. [PMID: 36366981 DOI: 10.1002/jmv.28299] [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] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
Monkeypox virus (MPXV) is a member of Orthopoxvirus in the Poxviridae family, causing a Public Health Emergency of International Concern. The number of cases and geographic range has increased significantly in 2022. Identification of MPXV-specific therapeutic targets is urgent. G-quadruplex (GQ) secondary structures attract great attention as potential targets for antiviral strategy. Whether GQs are present in the MPXV genome remains inconclusive. In this study, we aim to characterize the GQs encoded by MPXV. Through a series of biophysical experiments, we characterized the formation potential of MPXV-encoded GQs and evaluated the binding and stabilization abilities of GQ ligands including BRACO-19, pyridostatin, and TMPyP4 to GQs encoded by MPXV. Moreover, GQ ligands suppressed the gene transcription of MPXV sequences containing GQ. BRACO-19 and TMPyP4 were able to inhibit vaccinia virus replication. We demonstrated the existence of MPXV GQ and reinforced the idea that GQs could be novel antiviral targets. Targeting these GQ sequences with GQ-binding molecules may represent a new approach for MPXV therapy.
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Affiliation(s)
- Lu Lv
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.,Institute of Infection and Immunity, Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Infectious Diseases, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.,Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.,Institute of Infection and Immunity, Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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5
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Shankar U, Mishra SK, Jain N, Tawani A, Yadav P, Kumar A. Ni +2 permease system of Helicobacter pylori contains highly conserved G-quadruplex motifs. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105298. [PMID: 35526824 DOI: 10.1016/j.meegid.2022.105298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
The genome of a micro-organism contains all the information required for its survival inside its host cells. The guanine rich regions of the genome can form stable G-quadruplex structures that act as the regulators of gene expression. Herein, the completely sequenced genomes of Helicobacter pylori were explored for the identification and characterization of the conserved G-quadruplex motifs in this gastrointestinal pathogen. Initial in silico analysis revealed the presence of ~8241 GQ motifs in the H. pylori genome. Metal binding proteins of H. pylori are significantly enriched in the GQ motifs. Our study emphasizes the identification and characterization of four highly conserved G-quadruplex forming motifs (HPGQs) in the nickel transporter genes (nixA, niuB1, niuB2, and niuD) of the H. pylori. Nickel is a virulence determinant in H. pylori and is required as a co-factor for the urease and [NiFe] hydrogenase enzymes that are crucial for its survival in the stomach lining of humans. The presence of GQ motifs in these nickel transporter genes can affect their expression and may alter the functioning of Urease and [NiFe] hydrogenase. Similar to human and virus G-quadruplexes, targeting these conserved PGQs with bioactive molecules may represent a novel therapeutic avenue for combating infection of H. pylori. The identified HPGQs were characterized in-vitro by using CD spectroscopy, electrophoresis technique, and NMR spectroscopy at both acidic (4.5) and neutral pH (7.0). ITC revealed the specific interaction of these HPGQs with high affinity to the known G-quadruplex binding ligand, TMPyP4. The mTFP based reporter assay showed decrease in the gene expression of mTFP in the TMPyP4 treated cells as compared to the untreated and further affirmed the formation of stable G-quadruplex structures in the HPGQ motifs in vivo. This is the first report for characterizing G-quadruplex motifs in nickel transport-associated genes in the H. pylori bacterium.
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Affiliation(s)
- Uma Shankar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Subodh Kumar Mishra
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Arpita Tawani
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India.
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Characterization of G-Quadruplexes in Enterovirus A71 Genome and Their Interaction with G-Quadruplex Ligands. Microbiol Spectr 2022; 10:e0046022. [PMID: 35446122 PMCID: PMC9241713 DOI: 10.1128/spectrum.00460-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human enteroviruses cause many diseases; however, there is no specific therapeutic drug. G-quadruplex is an atypical secondary structure formed in the guanine rich region of DNA or RNA, which can exist in the viral genome. The different positions of G-quadruplex play an important role in the regulation of virus replication and infection. Whether G-quadruplexes are present in human enteroviruses is unknown. In current study, we analyzed the potential quadruplex forming sequences of human enteroviruses, especially EV-A71 virus, which causes hand, foot, and mouth disease. The results showed that there were a certain number of potential quadruplex-forming sequences in human enteroviruses. Through a variety of experimental methods, we evaluated the formation potential of EV-A71 encoded G-quadruplex and analyzed the binding ability of G-quadruplex ligands, including BRACO-19, pyridostatin and TMPyP4 to virus encoded G-quadruplexes. G-quadruplex ligands BRACO-19, PDS and TMPyP4 could inhibit the transcription of constructs containing EV-A71 G-quadruplex sequences. Moreover, we found that BRACO-19 was able to inhibit the replication of EV-A71, suggesting that targeting G-quadruplexes in EV-A71 genome by G-quadruplex ligands could be a novel antiviral way against EV-A71. Our finding not only uncovered the G-quadruplexes in human enteroviruses, but also would provide a new strategy for human enteroviruses therapy. IMPORTANCE G-quadruplex is a stable nucleic acid secondary structure formed by the folding of guanine rich nucleic acid. The important regulatory function of G-quadruplex makes it an attractive target of antiviral effect. Human enteroviruses cause a variety of human diseases, including common cold, nervous system diseases, cardiovascular damage, and diabetes. Enterovirus A71 (EV-A71) is one of pathogens causing hand, foot, and mouth disease; however, whether G-quadruplexes are present in the genomes of human enteroviruses is unknown. The function of G-quadruplexes in the EV-A71 genomes is not clear. We predicted and characterized G-quadruplex sequences in EV-A71. G-quadruplex ligands were identified to stabilize EV-A71 G-quadruplexes with high affinities. We also demonstrated G-quadruplex ligand BRACO-19 inhibited EV-A71 replication. Our studies provide a framework for targeting G-quadruplexes in the enteroviruses genome, which will be a new way to develop antiviral agents against human enteroviruses.
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Abstract
The noncanonical structures, G-quadruplexes (GQs), formed in the guanine-rich region of nucleic acids regulate various biological and molecular functions in prokaryotes and eukaryotes. Neisseria meningitidis is a commensal residing in a human's upper respiratory tract but occasionally becomes virulent, causing life-threatening septicemia and meningitis. The factors causing these changes in phenotypes are not fully understood. At the molecular level, regulatory components help in a clearer understanding of the pathogen's virulence and pathogenesis. Herein, genome analysis followed by biophysical assays and cell-based experiments revealed the presence of conserved GQ motifs in N. meningitidis. These GQs are linked to the essential genes involved in cell adhesion, pathogenesis, virulence, transport, DNA repair, and recombination. Primer extension stop assay, reporter assays, and quantitative real-time polymerase chain reaction (qRT-PCR) further affirmed the formation of stable GQs in vitro and in vivo. These results support the existence of evolutionarily conserved GQ motifs in N. meningitidis and uphold the usage of GQ-specific ligands as novel antimeningococcal therapeutics.
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Feng G, Zhang D, Peng C, Wu M, Xiao P, Li N. Study on the Anti-Adenovirus Mechanism of Sargassum fusiforme. Front Cell Infect Microbiol 2022; 12:860559. [PMID: 35321314 PMCID: PMC8936137 DOI: 10.3389/fcimb.2022.860559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Human adenovirus (HAdV) has a worldwide distribution and remains a major pathogen that leads to infections of the respiratory tract. No specific treatments or vaccines are yet available for HAdV infection. Sargassum fusiforme, an edible seaweed, has attracted a lot of attention for its various bioactivities. S. fusiforme has been reported to exhibit antiviral activity. However, research studies about its anti-HAdV activity are few. In this research, we found that S. fusiforme had low cytotoxicity and possessed anti-human adenovirus type 7 (HAdV7) activity in vitro, and the most effective ingredient was alginate. The time of addition assay demonstrated inhibitory effects that were observed in all life stages of the virus. In addition, we observed that the antiviral activity of alginate against HAdV7 infection might be closely related to the endoplasmic reticulum stress (ERS) pathway. Taken together, these results suggest that S. fusiforme extracts have potential application in the prevention and treatment of HAdV infection.
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Affiliation(s)
- Guanrong Feng
- Institute of Virology, Wenzhou University, Wenzhou, China
- Key Laboratory of Virology and Immunology of Wenzhou, Wenzhou University, Wenzhou, China
| | - Duo Zhang
- Institute of Virology, Wenzhou University, Wenzhou, China
- Key Laboratory of Virology and Immunology of Wenzhou, Wenzhou University, Wenzhou, China
| | - Chengcheng Peng
- Institute of Virology, Wenzhou University, Wenzhou, China
- Key Laboratory of Virology and Immunology of Wenzhou, Wenzhou University, Wenzhou, China
| | - Mingjiang Wu
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Pengpeng Xiao
- Institute of Virology, Wenzhou University, Wenzhou, China
- Key Laboratory of Virology and Immunology of Wenzhou, Wenzhou University, Wenzhou, China
| | - Nan Li
- Institute of Virology, Wenzhou University, Wenzhou, China
- Key Laboratory of Virology and Immunology of Wenzhou, Wenzhou University, Wenzhou, China
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Piperine analogs arrest c-myc gene leading to downregulation of transcription for targeting cancer. Sci Rep 2021; 11:22909. [PMID: 34824301 PMCID: PMC8617303 DOI: 10.1038/s41598-021-01529-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/28/2021] [Indexed: 11/08/2022] Open
Abstract
G-quadruplex (G4) structures are considered a promising therapeutic target in cancer. Since Ayurveda, Piperine has been known for its medicinal properties. Piperine shows anticancer properties by stabilizing the G4 motif present upstream of the c-myc gene. This gene belongs to a group of proto-oncogenes, and its aberrant transcription drives tumorigenesis. The transcriptional regulation of the c-myc gene is an interesting approach for anticancer drug design. The present study employed a chemical similarity approach to identify Piperine similar compounds and analyzed their interaction with cancer-associated G-quadruplex motifs. Among all Piperine analogs, PIP-2 exhibited strong selectivity, specificity, and affinity towards c-myc G4 DNA as elaborated through biophysical studies such as fluorescence emission, isothermal calorimetry, and circular dichroism. Moreover, our biophysical observations are supported by molecular dynamics analysis and cellular-based studies. Our study showed that PIP-2 showed higher toxicity against the A549 lung cancer cell line but lower toxicity towards normal HEK 293 cells, indicating increased efficacy of the drug at the cellular level. Biological evaluation assays such as TFP reporter assay, quantitative real-time PCR (qRT- PCR), and western blotting suggest that the Piperine analog-2 (PIP-2) stabilizes the G-quadruplex motif located at the promoter site of c-myc oncogene and downregulates its expression. In conclusion, Piperine analog PIP-2 may be used as anticancer therapeutics as it affects the c-myc oncogene expression via G-quadruplex mediated mechanism.
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Ruggiero E, Zanin I, Terreri M, Richter SN. G-Quadruplex Targeting in the Fight against Viruses: An Update. Int J Mol Sci 2021; 22:ijms222010984. [PMID: 34681641 PMCID: PMC8538215 DOI: 10.3390/ijms222010984] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of key cellular processes, such as transcription and replication. Since their discovery, G4s have been mainly investigated for their role in cancer and as targets in anticancer therapy. More recently, exploration of the presence and role of G4s in viral genomes has led to the discovery of G4-regulated key viral pathways. In this context, employment of selective G4 ligands has helped to understand the complexity of G4-mediated mechanisms in the viral life cycle, and highlighted the possibility to target viral G4s as an emerging antiviral approach. Research in this field is growing at a fast pace, providing increasing evidence of the antiviral activity of old and new G4 ligands. This review aims to provide a punctual update on the literature on G4 ligands exploited in virology. Different classes of G4 binders are described, with emphasis on possible antiviral applications in emerging diseases, such as the current COVID-19 pandemic. Strengths and weaknesses of G4 targeting in viruses are discussed.
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Pandya N, Jain N, Kumar A. Interaction analysis of anti-cancer drug Methotrexate with bcl-2 promoter stabilization and its transcription regulation. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Warner EF, Bohálová N, Brázda V, Waller ZAE, Bidula S. Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets? Microb Genom 2021; 7:000570. [PMID: 33956596 PMCID: PMC8209732 DOI: 10.1099/mgen.0.000570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 12/26/2022] Open
Abstract
Fungal infections cause >1 million deaths annually and the emergence of antifungal resistance has prompted the exploration for novel antifungal targets. Quadruplexes are four-stranded nucleic acid secondary structures, which can regulate processes such as transcription, translation, replication and recombination. They are also found in genes linked to virulence in microbes, and ligands that bind to quadruplexes can eliminate drug-resistant pathogens. Using a computational approach, we quantified putative quadruplex-forming sequences (PQS) in 1359 genomes across the fungal kingdom and explored their presence in genes related to virulence, drug resistance and biological processes associated with pathogenicity in Aspergillus fumigatus. Here we present the largest analysis of PQS in fungi and identify significant heterogeneity of these sequences throughout phyla, genera and species. PQS were genetically conserved in Aspergillus spp. and frequently pathogenic species appeared to contain fewer PQS than their lesser/non-pathogenic counterparts. GO-term analysis identified that PQS-containing genes were involved in processes linked with virulence such as zinc ion binding, the biosynthesis of secondary metabolites and regulation of transcription in A. fumigatus. Although the genome frequency of PQS was lower in A. fumigatus, PQS could be found enriched in genes involved in virulence, and genes upregulated during germination and hypoxia. Moreover, PQS were found in genes involved in drug resistance. Quadruplexes could have important roles within fungal biology and virulence, but their roles require further elucidation.
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Affiliation(s)
- Emily F. Warner
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Present address: Ikarovec Limited, Norwich Research Park Innovation Centre, Norwich, UK
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | | | - Stefan Bidula
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Bohálová N, Cantara A, Bartas M, Kaura P, Šťastný J, Pečinka P, Fojta M, Mergny JL, Brázda V. Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection. Biochimie 2021; 186:13-27. [PMID: 33839192 DOI: 10.1016/j.biochi.2021.03.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022]
Abstract
G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5'UTRs and 3'UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.
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Affiliation(s)
- Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Alessio Cantara
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Patrik Kaura
- Brno University of Technology, Faculty of Mechanical Engineering, Technická 2896/2, 616 69, Brno, Czech Republic
| | - Jiří Šťastný
- Brno University of Technology, Faculty of Mechanical Engineering, Technická 2896/2, 616 69, Brno, Czech Republic; Department of Informatics, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 612 65, Czech Republic.
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Shankar U, Jain N, Majee P, Kodgire P, Sharma TK, Kumar A. Exploring Computational and Biophysical Tools to Study the Presence of G-Quadruplex Structures: A Promising Therapeutic Solution for Drug-Resistant Vibrio cholerae. Front Genet 2020; 11:935. [PMID: 33101360 PMCID: PMC7545536 DOI: 10.3389/fgene.2020.00935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
Vibrio cholerae, a gram-negative bacterium that causes cholera, has already caused seven major pandemics across the world and infects roughly 1.3–4 million people every year. Cholera treatment primarily involves oral rehydration therapy supplemented with antibiotics. But recently, multidrug-resistant strains of V. cholerae have emerged. High genomic plasticity further enhances the pathogenesis of this human pathogen. Guanines in DNA or RNA assemble to form G-quadruplex (GQ) structures which have begun to be seen as potential drug targeting sites for different pathogenic bacteria and viruses. In this perspective, we carried out a genome-wide hunt in V. cholerae using a bio-informatics approach and observed ∼85 G-quadruplex forming motifs (VC-PGQs) in chromosome I and ∼45 putative G-quadruplexs (PGQs) in chromosome II. Ten putative G-quadruplex forming motifs (VC-PGQs) were selected on the basis of conservation throughout the genus and functional analysis displayed their location in the essential genes encoding bacterial proteins, for example, methyl-accepting chemotaxis protein, orotate phosphoribosyl transferase protein, amidase proteins, etc. The predicted VC-PGQs were validated using different bio-physical techniques, including Nuclear Magnetic Resonance spectroscopy, Circular Dichroism spectroscopy, and electrophoretic mobility shift assay, which demonstrated the formation of highly stable GQ structures in the bacteria. The interaction of these VC-PGQs with the known specific GQ ligand, TMPyP4, was analyzed using ITC and molecular dynamics studies that displayed the stabilization of the VC-PGQs by the GQ ligands and thus represents a potential therapeutic strategy against this enteric pathogen by inhibiting the PGQ harboring gene expression, thereby inhibiting the bacterial growth and virulence. In summary, this study reveals the presence of conserved GQ forming motifs in the V. cholerae genome that has the potential to be used to treat the multi-drug resistance problem of the notorious enteric pathogen.
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Affiliation(s)
- Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Prativa Majee
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | | | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Jain N, Mishra SK, Shankar U, Jaiswal A, Sharma TK, Kodgire P, Kumar A. G-quadruplex stabilization in the ions and maltose transporters gene inhibit Salmonella enterica growth and virulence. Genomics 2020; 112:4863-4874. [PMID: 32898642 PMCID: PMC7474834 DOI: 10.1016/j.ygeno.2020.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/15/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
The G-quadruplex structure is a highly conserved drug target for preventing infection of several human pathogens. We tried to explore G-quadruplex forming motifs as promising drug targets in the genome of Salmonella enterica that causes enteric fever in humans. Herein, we report three highly conserved G-quadruplex motifs (SE-PGQ-1, 2, and 3) in the genome of Salmonella enterica. Bioinformatics analysis inferred the presence of SE-PGQ-1 in the regulatory region of mgtA, SE-PGQ-2 in ORF of entA, and SE-PGQ-3 in the promoter region of malE and malK genes. The G-quadruplex forming sequences were confirmed by biophysical and biomolecular techniques. Cellular studies affirm the inhibitory effect of G-quadruplex specific ligands on Salmonella enterica growth. Further, PCR inhibition, reporter based assay, and RT-qPCR assays emphasize the biological relevance of G-quadruplexes in these genes. Thus, this study confirmed the presence of G-quadruplex motifs in Salmonella enterica and characterized them as a promising drug target.
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Affiliation(s)
- Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Ankit Jaiswal
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India.
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Shankar U, Jain N, Mishra SK, Sharma TK, Kumar A. Conserved G-Quadruplex Motifs in Gene Promoter Region Reveals a Novel Therapeutic Approach to Target Multi-Drug Resistance Klebsiella pneumoniae. Front Microbiol 2020; 11:1269. [PMID: 32714288 PMCID: PMC7344255 DOI: 10.3389/fmicb.2020.01269] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/19/2020] [Indexed: 11/22/2022] Open
Abstract
An opportunistic pathogen, Klebsiella pneumoniae is known to cause life-threating nosocomial infection with a high rate of morbidity and mortality. Evolutions of multi-drug-resistant and hyper-virulent strains of K. pneumoniae make the situation worse. Currently, there is no incisive drug molecule available for drug-resistant hyper-virulent K. pneumoniae infection that emphasizes the need for identification of novel and more promising drug targets in K. pneumoniae. Recently, various non-canonical structures of nucleic acids especially G-quadruplex (G4) motifs have been identified as potential therapeutic targets against several human pathogenic bacteria and viruses including Mycobacterium tuberculosis, Streptococcus pneumoniae, human immunodeficiency virus (HIV), Ebola, and Nipah. Therefore, in present study we screened the K. pneumoniae genomes for identification of evolutionary conserved G4 structure-forming motifs as promising anti-bacterial drug targets. Bioinformatics analysis revealed the presence of six highly conserved G4 motifs in the promoter region of five essential genes that play a critical role in nutrient transport and metabolism. Biophysical studies showed the formation of G4 structure by these conserved motifs. Circular Dichroism melting analysis showed the stabilization of these G4 motifs by a well-known G4-stabilizing agent, BRACO-19. The stabilization of these motifs by BRACO-19 was also able to stop the primer extension process, which is an essential phenomenon for expression of the G4-harboring gene. The addition of G4-specific ligand at low micromolar range was observed to be lethal for the growth of this bacteria and negatively controlled the expression of the G4-harboring genes via G4 structure stabilization. These observations strengthen the formation of G4 structures by the predicted G4 motif in vivo, which can be stabilized by G4 ligands like BRACO-19. This stabilization of G4 structures can attenuate the expression of G4-harboring essential genes and thus play a critical role in the regulation of gene expression. Thus, taking all given result in consideration, for the first time, this study showed the new therapeutic avenue for combating K. pneumoniae infection by characterizing the conserved G4 motifs as promising therapeutic targets.
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Affiliation(s)
- Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | | | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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