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Qiu TX, Liu L, Wang H, Hu Y, Chen J. Schisandrin A: A sustainable antiviral and immunomodulatory agent against spring viraemia of carp virus in aquaculture. FISH & SHELLFISH IMMUNOLOGY 2024; 154:109914. [PMID: 39306214 DOI: 10.1016/j.fsi.2024.109914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 09/14/2024] [Accepted: 09/18/2024] [Indexed: 09/26/2024]
Abstract
Spring viraemia of carp virus (SVCV) is a major threat to the aquaculture industry, causing severe economic losses and significantly impacting fish health. Despite this, no approved antiviral treatments are currently available for use in aquaculture, underscoring the urgent need for effective interventions. This study evaluated the antiviral and immunomodulatory potential of Schisandrin A (SA), a bioactive compound derived from the traditional Chinese medicinal herb Schisandra chinensis, against SVCV. Through a combination of in vitro and in vivo experiments, SA was found to significantly inhibit SVCV replication, lower the viral titer, and improve survival rates in infected juvenile carp. Mechanistically, SA enhanced the host's innate immune response, as demonstrated by the upregulation of key antiviral genes including interferon-alpha1 (ifna1), interferon-gamma (ifnγ), interferon-stimulated gene 15 (isg15), and myxovirus resistance 1 (mx1). Additionally, SA exhibited potent antioxidative properties, preserving mitochondrial integrity and reducing oxidative stress in SVCV-infected cells. These findings showed the dual role of SA in both directly suppressing viral replication and modulating the immune response, offering a multifaceted approach to managing SVCV infection. Given its low toxicity and biodegradability, SA emerges as a promising, sustainable antiviral agent for aquaculture. This study highlights the potential of SA to enhance biosecurity and promote sustainability in the industry, paving the way for the development of eco-friendly antivirals that could improve the management of viral diseases, ensuring healthier fish populations and greater economic stability.
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Affiliation(s)
- Tian-Xiu Qiu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China
| | - Lei Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China.
| | - Huan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China
| | - Yang Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo, 315832, China.
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Yin Z(S, Wang Z. Strategies for engineering oncolytic viruses to enhance cancer immunotherapy. Front Pharmacol 2024; 15:1450203. [PMID: 39309012 PMCID: PMC11413971 DOI: 10.3389/fphar.2024.1450203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/30/2024] [Indexed: 09/25/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is the predominant form of lung cancer and is characterized by rapid metastasis and high mortality, presenting a challenge for early-stage treatment modalities. The heterogeneity of NSCLC's tumor microenvironment (TME) significantly influences the efficacy of anti-PD-1 immune checkpoint inhibitors (ICIs) therapy, leading to varied patient responses. This review characterized different strains of oncolytic viruses in NSCLC and the different gene edits in pre-existing oncolytic viruses. This study also aimed to provide strategies to enhance anti-PD-1 therapy in NSCLC by engineering oncolytic viruses (OVs). This study offers insights into the genomic adaptations necessary for OVs targeting NSCLC, identify genetic determinants of anti-PD-1 response variability, and propose genomic edits to bolster therapy effectiveness. The primary goal of this study is to present a theoretically designed OV with a detailed genomic framework capable of enhancing the response to anti-PD-1 therapy, thereby advancing the field of cancer immunotherapy.
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Affiliation(s)
| | - Zhengfeng Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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3
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McGraw A, Hillmer G, Choi J, Narayan K, Mehedincu SM, Marquez D, Tibebe H, DeCicco-Skinner KL, Izumi T. Evaluating HIV-1 Infectivity and Virion Maturation across Varied Producer Cells with a Novel FRET-Based Detection and Quantification Assay. Int J Mol Sci 2024; 25:6396. [PMID: 38928103 PMCID: PMC11204348 DOI: 10.3390/ijms25126396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
The maturation of HIV-1 virions is a crucial process in viral replication. Although T-cells are a primary source of virus production, much of our understanding of virion maturation comes from studies using the HEK293T human embryonic kidney cell line. Notably, there is a lack of comparative analyses between T-cells and HEK293T cells in terms of virion maturation efficiency in existing literature. We previously developed an advanced virion visualization system based on the FRET principle, enabling the effective distinction between immature and mature virions via fluorescence microscopy. In this study, we utilized pseudotyped, single-round infectious viruses tagged with FRET labels (HIV-1 Gag-iFRET∆Env) derived from Jurkat (a human T-lymphocyte cell line) and HEK293T cells to evaluate their virion maturation rates. HEK293T-derived virions demonstrated a maturity rate of 81.79%, consistent with other studies and our previous findings. However, virions originating from Jurkat cells demonstrated a significantly reduced maturation rate of 68.67% (p < 0.0001). Correspondingly, viruses produced from Jurkat cells exhibited significantly reduced infectivity compared to those derived from HEK293T cells, with the relative infectivity measured at 65.3%. This finding is consistent with the observed relative maturation rate of viruses produced by Jurkat cells. These findings suggest that initiation of virion maturation directly correlates with viral infectivity. Our observation highlights the dynamic nature of virus-host interactions and their implications for virion production and infectivity.
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Affiliation(s)
- Aidan McGraw
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Grace Hillmer
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Jeongpill Choi
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Kedhar Narayan
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Stefania M. Mehedincu
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Dacia Marquez
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Hasset Tibebe
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Kathleen L. DeCicco-Skinner
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Taisuke Izumi
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
- District of Columbia Center for AIDS Research, Washington, DC 20052, USA
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McGraw A, Hillmer G, Choi J, Narayan K, Marquez D, Tibebe H, Izumi T. Evaluating HIV-1 Infectivity and Virion Maturation Across Varied Producer Cells with a Novel FRET-Based Detection and Quantification Assay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.25.573317. [PMID: 38234844 PMCID: PMC10793453 DOI: 10.1101/2023.12.25.573317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The maturation of HIV-1 virions is a crucial process in viral replication. Although T cells are a primary source of virus production, much of our understanding of virion maturation comes from studies using the HEK293T human embryonic kidney cell line. Notably, there is a lack of comparative analyses between T cells and HEK293T cells in terms of virion maturation efficiency in existing literature. We previously developed an advanced virion visualization system based on the FRET principle, enabling the effective distinction between immature and mature virions via fluorescence microscopy. In this study, we utilized pseudotyped, single-round infectious viruses tagged with FRET labels (HIV-1 Gag-iFRETΔEnv) derived from Jurkat (a human T lymphocyte cell line) and HEK293T cells to evaluate their virion maturation rates. HEK293T-derived virions demonstrated a maturity rate of 81.79%, consistent with other studies and our previous findings. However, virions originating from Jurkat cells demonstrated a significantly reduced maturation rate of 68.67% (p < 0.0001). Correspondingly, viruses produced from Jurkat cells exhibited significantly reduced infectivity compared to those derived from HEK293T cells, with the relative infectivity measured at 65.3%. This finding is consistent with the observed relative maturation rate of viruses produced by Jurkat cells. These findings suggest that initiation of virion maturation directly correlates with viral infectivity. Our observation highlights the dynamic nature of virus-host interactions and their implications for virion production and infectivity.
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Zia S, Sumon MM, Ashik MA, Basar A, Lim S, Oh Y, Park Y, Rahman MM. Potential Inhibitors of Lumpy Skin Disease's Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches. Animals (Basel) 2024; 14:1283. [PMID: 38731287 PMCID: PMC11083254 DOI: 10.3390/ani14091283] [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: 03/01/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024] Open
Abstract
Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle. This spreads through direct contact and insect vectors, significantly affecting global cattle farming. Despite the availability of vaccines, their efficacy is limited by poor prophylaxis and adverse effects. Our study aimed to identify the potential inhibitors targeting the LSDV-encoded DNA polymerase protein (gene LSDV039) for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as being potent binders among 380 phytocompounds, with respective affinities of -8.97 and -7.20 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.86 and -8.86 kcal/mol) among 718 FDA-approved antiviral drugs. Simulating the molecular dynamics of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF, but fluctuated in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. This study highlights the promising potential of using repurposed drugs and phytocompounds as potential LSD therapeutics. However, extensive validation through in vitro and in vivo testing and clinical trials is crucial for their practical application.
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Affiliation(s)
- Sabbir Zia
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Md-Mehedi Sumon
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Md-Ashiqur Ashik
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Abul Basar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Sangjin Lim
- College of Forest & Environmental Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Yeonsu Oh
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Yungchul Park
- College of Forest & Environmental Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Md-Mafizur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
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Jiao Y, Shi C, Sun Y. The use of Xuanbai Chengqi decoction on monkeypox disease through the estrone-target AR interaction. Front Microbiol 2023; 14:1234817. [PMID: 37808322 PMCID: PMC10553791 DOI: 10.3389/fmicb.2023.1234817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction After COVID-19, there was an outbreak of a new infectious disease caused by monkeypox virus. So far, no specific drug has been found to treat it. Xuanbai Chengqi decoction (XBCQD) has shown effects against a variety of viruses in China. Methods We searched for the active compounds and potential targets for XBCQD from multiple open databases and literature. Monkeypox related targets were searched out from the OMIM and GeneCards databases. After determining the assumed targets of XBCQD for monkeypox treatment, we built the PPI network and used R for GO enrichment and KEGG pathway analysis. The interactions between the active compounds and the hub targets were investigated by molecular docking and molecular dynamics (MD) simulations. Results In total, 5 active compounds and 10 hub targets of XBCQD were screened out. GO enrichment and KEGG analysis demonstrated that XBCQD plays a therapeutic role in monkeypox mainly by regulating signaling pathways related to viral infection and inflammatory response. The main active compound estrone binding to target AR was confirmed to be the best therapy choice for monkeypox. Discussion This study systematically explored the interactions between the bioactive compounds of XBCQD and the monkeypox-specific XBCQD targets using network pharmacological methods, bioinformatics analyses and molecular simulations, suggesting that XBCQD could have a beneficial therapeutic effect on monkeypox by reducing the inflammatory damage and viral replication via multiple pathways. The use of XBCQD on monkeypox disease was confirmed to be best worked through the estrone-target AR interaction. Our work could provide evidence and guidance for further research on the treatment of monkeypox disease.
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Affiliation(s)
- Yanqi Jiao
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Chengcheng Shi
- School of Science/State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology (Shenzhen), Shenzhen, China
| | - Yao Sun
- School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, China
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Rashmi SH, Disha KS, Sudheesh N, Karunakaran J, Joseph A, Jagadesh A, Mudgal PP. Repurposing of approved antivirals against dengue virus serotypes: an in silico and in vitro mechanistic study. Mol Divers 2023:10.1007/s11030-023-10716-5. [PMID: 37632595 DOI: 10.1007/s11030-023-10716-5] [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: 07/03/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Dengue is an emerging, mosquito-borne viral disease of international public health concern. Dengue is endemic in more than 100 countries across the world. However, there are no clinically approved antivirals for its cure. Drug repurposing proves to be an efficient alternative to conventional drug discovery approaches in this regard, as approved drugs with an established safety profile are tested for new indications, which circumvents several time-consuming experiments. In the present study, eight approved RNA-dependent RNA polymerase inhibitors of Hepatitis C virus were virtually screened against the Dengue virus polymerase protein, and their antiviral activity was assessed in vitro. Schrödinger software was used for in silico screening, where the compounds were passed through several hierarchical filters. Among the eight compounds, dasabuvir was finally selected for in vitro cytotoxicity and antiviral screening. Cytotoxicity profiling of dasabuvir in Vero cells revealed changes in cellular morphology, cell aggregation, and detachment at 50 μM. Based on these results, four noncytotoxic concentrations of dasabuvir (0.1, 0.25, 0.5, and 1 µM) were selected for antiviral screening against DENV-2 under three experimental conditions: pre-infection, co-infection, and post-infection treatment, by plaque reduction assay. Viral plaques were reduced significantly (p < 0.05) in the co-infection and post-infection treatment regimens; however, no reduction was observed in the pretreatment group. This indicated a possible interference of dasabuvir with NS5 RdRp, as seen from in silico interaction studies, translating into a reduction in virus plaques. Such studies reiterate the usefulness of drug repurposing as a viable strategy in antiviral drug discovery. In this drug repurposing study, dasabuvir, a known anti-hepatitis C drug, was selected through virtual screening and assessed for its anti-dengue activity.
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Affiliation(s)
- S H Rashmi
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - K Sai Disha
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - N Sudheesh
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Joseph Karunakaran
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Anitha Jagadesh
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - P P Mudgal
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India.
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Patel P, Nandi A, Verma SK, Kaushik N, Suar M, Choi EH, Kaushik NK. Zebrafish-based platform for emerging bio-contaminants and virus inactivation research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162197. [PMID: 36781138 PMCID: PMC9922160 DOI: 10.1016/j.scitotenv.2023.162197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 05/27/2023]
Abstract
Emerging bio-contaminants such as viruses have affected health and environment settings of every country. Viruses are the minuscule entities resulting in severe contagious diseases like SARS, MERS, Ebola, and avian influenza. Recent epidemic like the SARS-CoV-2, the virus has undergone mutations strengthen them and allowing to escape from the remedies. Comprehensive knowledge of viruses is essential for the development of targeted therapeutic and vaccination treatments. Animal models mimicking human biology like non-human primates, rats, mice, and rabbits offer competitive advantage to assess risk of viral infections, chemical toxins, nanoparticles, and microbes. However, their economic maintenance has always been an issue. Furthermore, the redundancy of experimental results due to aforementioned aspects is also in examine. Hence, exploration for the alternative animal models is crucial for risk assessments. The current review examines zebrafish traits and explores the possibilities to monitor emerging bio-contaminants. Additionally, a comprehensive picture of the bio contaminant and virus particle invasion and abatement mechanisms in zebrafish and human cells is presented. Moreover, a zebrafish model to investigate the emerging viruses such as coronaviridae and poxviridae has been suggested.
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Affiliation(s)
- Paritosh Patel
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea
| | - Aditya Nandi
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Suresh K Verma
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India; Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, 18323 Hwaseong, Republic of Korea
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
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Delgado-Maldonado T, Moreno-Herrera A, Pujadas G, Vázquez-Jiménez LK, González-González A, Rivera G. Recent advances in the development of methyltransferase (MTase) inhibitors against (re)emerging arboviruses diseases dengue and Zika. Eur J Med Chem 2023; 252:115290. [PMID: 36958266 DOI: 10.1016/j.ejmech.2023.115290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/22/2023]
Abstract
Emerging and/or re-emerging viral diseases such as dengue and Zika are a worldwide concern. Therefore, new antiviral therapeutics are necessary. In this sense, a non-structural protein with methyltransferase (MTase) activity is an attractive drug target because it plays a crucial role in dengue and Zika virus replication. Different drug strategies such as virtual screening, molecular docking, and molecular dynamics have identified new inhibitors that bind on the MTase active site. Therefore, in this review, we analyze MTase inhibitors, including S-adenosyl-L-methionine (SAM), S-adenosyl-l-homocysteine (SAH) and guanosine-5'-triphosphate (GTP) analogs, nitrogen-containing heterocycles (pyrimidine, adenosine, and pyridine), urea derivatives, and natural products. Advances in the design of MTase inhibitors could lead to the optimization of a possible single or broad-spectrum antiviral drug against dengue and Zika virus.
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Affiliation(s)
- Timoteo Delgado-Maldonado
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710, Reynosa, Mexico
| | - Antonio Moreno-Herrera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710, Reynosa, Mexico
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007, Tarragona, Catalonia, Spain
| | - Lenci K Vázquez-Jiménez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710, Reynosa, Mexico
| | - Alonzo González-González
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710, Reynosa, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, 88710, Reynosa, Mexico.
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Maddipati VC, Mittal L, Kaur J, Rawat Y, Koraboina CP, Bhattacharyya S, Asthana S, Gundla R. Discovery of non-nucleoside oxindole derivatives as potent inhibitors against dengue RNA-dependent RNA polymerase. Bioorg Chem 2023; 131:106277. [PMID: 36444792 DOI: 10.1016/j.bioorg.2022.106277] [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: 05/26/2022] [Revised: 10/20/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022]
Abstract
A series of thiazole linked Oxindole-5-Sulfonamide (OSA) derivatives were designed as inhibitors of RNA-dependent RNA polymerase (RdRp) activity of Dengue virus. These were synthesized and then evaluated for their efficacy in ex-vivo virus replication assay using human cell lines. Among 20 primary compounds in the series, OSA-15 was identified as a hit. A series of analogues were synthesized by replacing the difluoro benzyl group of OSA-15 with different substituted benzyl groups. The efficacy of OSA-15derivatives was less than that of the parent compound, except OSA-15-17, which has shown improved efficacy than OSA-15. The further optimization was carried out by adding dimethyl (DM) groups to both the sulfonamide and oxindole NH's to produce OSA-15-DM and OSA-15-17-DM. These two compounds were showing no detectable cytotoxicity and the latter was more efficacious. Further, both these compounds were tested for inhibition in all the serotypes of the Dengue virus using an ex-vivo assay. The EC50 of OSA-15-17-DM was observed in a low micromolar range between 2.5 and 5.0 µg/ml. Computation docking and molecular dynamics simulation studies confirmed the binding of identified hits to DENV RdRp. OSA15-17-DM blocks the RNA entrance and elongation site for their biological activity with high binding affinity. Overall, the identified oxindole derivatives are novel compounds that can inhibit Dengue replication, working as non-nucleoside inhibitors (NNI) to explore as anti-viral RdRp activity.
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Affiliation(s)
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3(rd)Milestone, Faridabad-Gurugram Expressway, Faridabad 121001, Haryana, India
| | - Jaskaran Kaur
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3(rd)Milestone, Faridabad-Gurugram Expressway, Faridabad 121001, Haryana, India
| | - Yogita Rawat
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3(rd)Milestone, Faridabad-Gurugram Expressway, Faridabad 121001, Haryana, India
| | - Chandra Prakash Koraboina
- Department of Chemistry, School of Science, GITAM (Deemed to be University) Hyderabad, Telangana 502 329, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3(rd)Milestone, Faridabad-Gurugram Expressway, Faridabad 121001, Haryana, India.
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3(rd)Milestone, Faridabad-Gurugram Expressway, Faridabad 121001, Haryana, India.
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM (Deemed to be University) Hyderabad, Telangana 502 329, India.
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Sepay N, Chakrabarti S, Afzal M, Alarifi A, Mal D. Identification of 4-acrylamido- N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study. RSC Adv 2022; 12:24178-24186. [PMID: 36128538 PMCID: PMC9403657 DOI: 10.1039/d2ra04333e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022] Open
Abstract
Omicron is one of the variants of COVID-19 and continuing member of a pandemic. There are several types of vaccines that were developed around the globe to fight against the virus. However, the world is suffering to find suitable drug candidates for the virus. The main protease (Mpro) enzyme of the virus is the best target for finding drug molecules because of its involvement in viral infection and protein synthesis. ZINC-15 is a database of 750 million commercially available compounds. We find 125 compounds having two aromatic rings and amide groups for non-covalent interactions with active site amino acids and functional groups with the capability to bind -SH group of C145 of Mpro through covalent bonding by a nucleophilic addition reaction. The lead compound (Z144) was identified using molecular docking. The non-covalent interactions (NCI) calculations show the interactions between amino acids present in the active site of the protein and the lead molecules are attractive in nature. The density functional-based tight-binding (DFTB) study of the lead compound with amino acids in the active site indicates that Q190 and Q193 play a very critical role in stabilization. The Michael addition of the acrylamide group of the lead molecule at β-position is facile because the low energy lowest unoccupied molecular orbital (LUMO) is concentrated on the group. From molecular dynamics during 100 ns, it has come to light that strong non-covalent interactions are key for the stability of the lead inside the protein and such binding can fold the protein. The free energy for this interaction is -42.72 kcal mol-1 which was obtained from MM-GB/SA calculations.
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Lady Brabourne College Kolkata 700017 India
| | | | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Dasarath Mal
- Department of Chemistry, Vijaygarh Jyotish Ray College Kolkata 700032 India
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12
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Bertini S, Alekseeva A, Elli S, Pagani I, Zanzoni S, Eisele G, Krishnan R, Maag KP, Reiter C, Lenhart D, Gruber R, Yates E, Vicenzi E, Naggi A, Bisio A, Guerrini M. Pentosan polysulfate inhibits attachment and infection by SARS-CoV-2 in vitro: insights into structural requirements for binding. Thromb Haemost 2022; 122:984-997. [PMID: 35322395 PMCID: PMC9252607 DOI: 10.1055/a-1807-0168] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Two years since the outbreak of the novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic, there remain few clinically effective drugs to complement vaccines. One is the anticoagulant, heparin, which in 2004 was found able to inhibit invasion of SARS-CoV (CoV-1) and which has been employed during the current pandemic to prevent thromboembolic complications and moderate potentially damaging inflammation. Heparin has also been shown experimentally to inhibit SARS-CoV-2 attachment and infection in susceptible cells. At high therapeutic doses however, heparin increases the risk of bleeding and prolonged use can cause heparin-induced thrombocytopenia, a serious side effect. One alternative, with structural similarities to heparin, is the plant-derived, semi-synthetic polysaccharide, pentosan polysulfate (PPS). PPS is an established drug for the oral treatment of interstitial cystitis, is well-tolerated, and exhibits weaker anticoagulant effects than heparin. In an established Vero cell model, PPS and its fractions of varying molecular weights inhibited invasion by SARS-CoV-2. Intact PPS and its size-defined fractions were characterized by molecular weight distribution and chemical structure using nuclear magnetic resonance spectroscopy and liquid chromatography–mass spectrometry, then employed to explore the structural basis of interactions with SARS-CoV-2 spike protein receptor-binding domain (S1 RBD) and the inhibition of Vero cell invasion. PPS was as effective as unfractionated heparin, but more effective in inhibiting cell infection than low-molecular-weight heparin (on a weight/volume basis). Isothermal titration calorimetry and viral plaque-forming assays demonstrated size-dependent binding to S1 RBD and inhibition of Vero cell invasion, suggesting the potential application of PPS as a novel inhibitor of SARS-CoV-2 infection.
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Affiliation(s)
- Sabrina Bertini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Anna Alekseeva
- Centro Alta Tecnologia Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Isabel Pagani
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Zanzoni
- Centro Piattaforme Tecnologiche, University of Verona, Verona, Italy
| | - Giorgio Eisele
- Centro Alta Tecnologia Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Ravi Krishnan
- Paradigm Biopharmaceuticals Ltd, Melbourne, Australia
| | - Klaus P Maag
- bene pharmaChem GmbH & Co.KG, Geretsried, Germany
| | | | | | | | - Edwin Yates
- Structural and Chemical Biology, University of Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland
| | - Elisa Vicenzi
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Annamaria Naggi
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Antonella Bisio
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
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13
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De Castro F, De Luca E, Benedetti M, Fanizzi FP. Platinum compounds as potential antiviral agents. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Liffner B, Absalon S. Expansion Microscopy Reveals Plasmodium falciparum Blood-Stage Parasites Undergo Anaphase with A Chromatin Bridge in the Absence of Mini-Chromosome Maintenance Complex Binding Protein. Microorganisms 2021; 9:2306. [PMID: 34835432 PMCID: PMC8620465 DOI: 10.3390/microorganisms9112306] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
The malaria parasite Plasmodium falciparum undergoes closed mitosis, which occurs within an intact nuclear envelope, and differs significantly from its human host. Mitosis is underpinned by the dynamics of microtubules and the nuclear envelope. To date, our ability to study P. falciparum mitosis by microscopy has been hindered by the small size of the P. falciparum nuclei. Ultrastructure expansion microscopy (U-ExM) has recently been developed for P. falciparum, allowing the visualization of mitosis at the individual nucleus level. Using U-ExM, three intranuclear microtubule structures are observed: hemispindles, mitotic spindles, and interpolar spindles. A previous study demonstrated that the mini-chromosome maintenance complex binding-protein (MCMBP) depletion caused abnormal nuclear morphology and microtubule defects. To investigate the role of microtubules following MCMBP depletion and study the nuclear envelope in these parasites, we developed the first nuclear stain enabled by U-ExM in P. falciparum. MCMBP-deficient parasites show aberrant hemispindles and mitotic spindles. Moreover, anaphase chromatin bridges and individual nuclei containing multiple microtubule structures were observed following MCMBP knockdown. Collectively, this study refines our understanding of MCMBP-deficient parasites and highlights the utility of U-ExM coupled with a nuclear envelope stain for studying mitosis in P. falciparum.
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Affiliation(s)
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
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15
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The Antiviral and Virucidal Activities of Voacangine and Structural Analogs Extracted from Tabernaemontana cymosa Depend on the Dengue Virus Strain. PLANTS 2021; 10:plants10071280. [PMID: 34201900 PMCID: PMC8309144 DOI: 10.3390/plants10071280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/21/2022]
Abstract
Currently, no specific licensed antiviral exists for treating the illness caused by dengue virus (DENV). Therefore, the search for compounds of natural origin with antiviral activity is an important area of research. In the present study, three compounds were isolated and identified from seeds of Tabernaemontana cymosa plants. The in vitro antiviral effect of those compounds and voacangine against different DENV strains was assessed using different experimental approaches: compounds added before the infection (Pre), at the same time with the virus (Trans), after the infection (Post) or compounds present in all moments of the experiment (Pre-Trans-Post, Combined treatment). In silico studies (docking and molecular dynamics) were also performed to explain the possible antiviral mechanisms. The identified compounds were three structural analogs of voacangine (voacangine-7-hydroxyindolenine, rupicoline and 3-oxo-voacangine). In the Pre-treatment, only voacangine-7-hydroxyindolenine and rupicoline inhibited the infection caused by the DENV-2/NG strain (16.4% and 29.6% infection, respectively). In the Trans-treatment approach, voacangine, voacangine-7-hydroxyindolenine and rupicoline inhibited the infection in both DENV-2/NG (11.2%, 80.4% and 75.7% infection, respectively) and DENV-2/16681 infection models (73.7%, 74.0% and 75.3% infection, respectively). The latter strain was also inhibited by 3-oxo-voacangine (82.8% infection). Moreover, voacangine (most effective virucidal agent) was also effective against one strain of DENV-1 (DENV-1/WestPac/74) and against the third strain of DENV-2 (DENV-2/S16803) (48.5% and 32.4% infection, respectively). Conversely, no inhibition was observed in the post-treatment approach. The last approach (combined) showed that voacangine, voacangine-7-hydroxyindolenine and rupicoline inhibited over 90% of infections (3.5%, 6.9% and 3.5% infection, respectively) of both strains (DENV-2/NG and DENV-2/16681). The free energy of binding obtained with an in silico approach was favorable for the E protein and compounds, which ranged between −5.1 and −6.3 kcal/mol. Finally, the complex formed between DENV-2 E protein and the best virucidal compound was stable for 50 ns. Our results show that the antiviral effect of indole alkaloids derived from T. cymose depends on the serotype and the virus strain.
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16
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Mushroom Nutrition as Preventative Healthcare in Sub-Saharan Africa. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11094221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The defining characteristics of the traditional Sub-Saharan Africa (SSA) cuisine have been the richness in indigenous foods and ingredients, herbs and spices, fermented foods and beverages, and healthy and whole ingredients used. It is crucial to safeguard the recognized benefits of mainstream traditional foods and ingredients, which gradually eroded in the last decades. Notwithstanding poverty, chronic hunger, malnutrition, and undernourishment in the region, traditional eating habits have been related to positive health outcomes and sustainability. The research prevailed dealing with food availability and access rather than the health, nutrition, and diet quality dimensions of food security based on what people consume per country and on the missing data related to nutrient composition of indigenous foods. As countries become more economically developed, they shift to “modern” occidental foods rich in saturated fats, salt, sugar, fizzy beverages, and sweeteners. As a result, there are increased incidences of previously unreported ailments due to an unbalanced diet. Protein-rich foods in dietary guidelines enhance only those of animal or plant sources, while rich protein sources such as mushrooms have been absent in these charts, even in developed countries. This article considers the valorization of traditional African foodstuffs and ingredients, enhancing the importance of establishing food-based dietary guidelines per country. The crux of this review highlights the potential of mushrooms, namely some underutilized in the SSA, which is the continent’s little exploited gold mine as one of the greatest untapped resources for feeding and providing income for Africa’s growing population, which could play a role in shielding Sub-Saharan Africans against the side effects of an unhealthy stylish diet.
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17
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Kumar V, Parate S, Yoon S, Lee G, Lee KW. Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2. Front Microbiol 2021; 12:647295. [PMID: 33967984 PMCID: PMC8097174 DOI: 10.3389/fmicb.2021.647295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/25/2021] [Indexed: 01/18/2023] Open
Abstract
The rapid spread of COVID-19, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a worldwide health emergency. Unfortunately, to date, a very small number of remedies have been to be found effective against SARS-CoV-2 infection. Therefore, further research is required to achieve a lasting solution against this deadly disease. Repurposing available drugs and evaluating natural product inhibitors against target proteins of SARS-CoV-2 could be an effective approach to accelerate drug discovery and development. With this strategy in mind, we derived Marine Natural Products (MNP)-based drug-like small molecules and evaluated them against three major target proteins of the SARS-CoV-2 virus replication cycle. A drug-like database from MNP library was generated using Lipinski's rule of five and ADMET descriptors. A total of 2,033 compounds were obtained and were subsequently subjected to molecular docking with 3CLpro, PLpro, and RdRp. The docking analyses revealed that a total of 14 compounds displayed better docking scores than the reference compounds and have significant molecular interactions with the active site residues of SARS-CoV-2 virus targeted proteins. Furthermore, the stability of docking-derived complexes was analyzed using molecular dynamics simulations and binding free energy calculations. The analyses revealed two hit compounds against each targeted protein displaying stable behavior, binding affinity, and molecular interactions. Our investigation identified two hit compounds against each targeted proteins displaying stable behavior, higher binding affinity and key residual molecular interactions, with good in silico pharmacokinetic properties, therefore can be considered for further in vitro studies.
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Affiliation(s)
- Vikas Kumar
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Shraddha Parate
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju, South Korea
| | - Sanghwa Yoon
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Gihwan Lee
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju, South Korea
| | - Keun Woo Lee
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
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18
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Kaur R, Kumar K. Synthetic and medicinal perspective of quinolines as antiviral agents. Eur J Med Chem 2021; 215:113220. [PMID: 33609889 PMCID: PMC7995244 DOI: 10.1016/j.ejmech.2021.113220] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/17/2020] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
In current scenario, various heterocycles have come up exhibiting crucial role in various medicinal agents which are valuable for mankind. Out of diverse range of heterocycle, quinoline scaffold have been proved to play an important role in broad range of biological activities. Several drug molecules bearing a quinoline molecule with useful anticancer, antibacterial activities etc have been marketed such as chloroquine, saquinavir etc. Owing to their broad spectrum biological role, various synthetic strategies such as Skraup reaction, Combes reaction etc. has been developed by the researchers all over the world. But still the synthetic methods are associated with various limitations as formation of side products, use of expensive metal catalysts. Thus, several efforts to develop an efficient and cost effective synthetic protocol are still carried out till date. Moreover, quinoline scaffold displays remarkable antiviral activity. Therefore, in this review we have made an attempt to describe recent synthetic protocols developed by various research groups along with giving a complete explanation about the role of quinoline derivatives as antiviral agent. Quinoline derivatives were found potent against various strains of viruses like zika virus, enterovirus, herpes virus, human immunodeficiency virus, ebola virus, hepatitis C virus, SARS virus and MERS virus etc.
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Affiliation(s)
- Ramandeep Kaur
- Department of Pharmaceutical Chemistry, Indo-Soviet Friendship College of Pharmacy (ISFCP), Moga, Punjab, 142001, India
| | - Kapil Kumar
- School of Pharmacy and Technology Management, SVKM's NMIMS, Hyderabad, Telangana, 509301, India.
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19
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ElBagoury M, Tolba MM, Nasser HA, Jabbar A, Elagouz AM, Aktham Y, Hutchinson A. The find of COVID-19 vaccine: Challenges and opportunities. J Infect Public Health 2021; 14:389-416. [PMID: 33647555 PMCID: PMC7773313 DOI: 10.1016/j.jiph.2020.12.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/30/2020] [Accepted: 12/20/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel corona virus, causing COVID-19 with Flu-like symptoms is the first alarming pandemic of the third millennium. SARS-CoV-2 belongs to beta coronavirus as Middle East respiratory syndrome coronavirus (MERS-CoV). Pandemic COVID-19 owes devastating mortality and destructively exceptional consequences on Socio-Economics life around the world. Therefore, the current review is redirected to the scientific community to owe comprehensive visualization about SARS-CoV-2 to tackle the current pandemic. As systematically shown through the current review, it indexes unmet medical problem of COVID-19 in view of public health and vaccination discovery for the infectious SARS-CoV-2; it is currently under-investigational therapeutic protocols, and next possible vaccines. Furthermore, the review extensively reports the precautionary measures to achieve" COVID-19/Flatten the curve". It is concluded that vaccines formulation within exceptional no time in this pandemic is highly recommended, via following the same protocols of previous pandemics; MERS-CoV and SARS-CoV, and excluding some initial steps of vaccination development process.
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Affiliation(s)
- Marwan ElBagoury
- University of South Wales, Pontypridd, Wales, United Kingdom; The Student Science and Technology Online Research Coop, Ontario, Canada.
| | - Mahmoud M Tolba
- Pharmaceutical division, ministry of health and population, Cairo, Egypt
| | - Hebatallah A Nasser
- Microbiology and Public Health Department, Faculty of Pharmacy, Heliopolis University, Cairo, Egypt
| | - Abdul Jabbar
- Department of Clinical Medicine, University of Veterinary and Animal Sciences, Lahore Punjab Pakistan
| | - Ahmed M Elagouz
- University of South Wales, Pontypridd, Wales, United Kingdom
| | - Yahia Aktham
- University of South Wales, Pontypridd, Wales, United Kingdom
| | - Amy Hutchinson
- The Student Science and Technology Online Research Coop, Ontario, Canada; McMaster University, Hamilton, Canada
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20
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Noor H, Ikram A, Rathinavel T, Kumarasamy S, Nasir Iqbal M, Bashir Z. Immunomodulatory and anti-cytokine therapeutic potential of curcumin and its derivatives for treating COVID-19 - a computational modeling. J Biomol Struct Dyn 2021; 40:5769-5784. [PMID: 33491580 DOI: 10.1080/07391102.2021.1873190] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The unavailability of vaccine and medicines raised serious issues during COVID-19 pandemic and peoples from different parts of world relied on traditional medicine for their immediate recovery from COVID-19 and it found effective also. The current research aims to target COVID-19 immunological human host receptors i.e. angiotensin-converting enzyme (ACE)-2, interleukin (IL)-1β, IL-6, tumor necrosis factor-alpha (TNF-α) and protease-activated receptor (PAR)-1 using curcumin derivatives to prevent viral infection and control overproduction of early clinical responses of COVID-19. Targeting these host proteins will mitigate the infection and will filter out many complications caused by these proteins in COVID-19 patients. It is proven through computer-aided computational modeling approaches, total 30 compounds of curcumin and its derivatives were chosen. Drug-likeness parameters were calculated for curcumin and its derivatives and 20 curcumin analogs were selected for docking analysis. From docking analysis of 20 curcumin analogs against five chosen human host receptor targets reveals 11 curcumin analogs possess least binding affinity and best interaction at active sites subjected to absorption, distribution, metabolism, excretion (ADME) analysis. Density functional theory (DFT) analysis of five final shortlisted curcumin derivatives was done to show least binding affinity toward chosen host target protein. Molecular dynamics simulation (MDS) was performed to observe behavior and interaction of potential drug hydrazinocurcumin against target proteins ACE-2 and PAR-1. It was performed at 100 nanoseconds and showed satisfactory results. Finally, our investigation reveals that hydrazinocurcumin possesses immunomodulatory and anti-cytokine therapeutic potential against COVID-19 and it can act as COVID-19 warrior drug molecule and promising choice of drug for COVID-19 treatment, however, it needs further in vivo clinical evaluation to commercialize as COVID-19 drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hasnat Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ayesha Ikram
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | | | | | - Muhammad Nasir Iqbal
- Department of Biosciences, COMSATS University, Islamabad Campus, Islamabad, Pakistan
| | - Zohaib Bashir
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
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21
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Zong Z, Zhang Z, Wu L, Zhang L, Zhou F. The Functional Deubiquitinating Enzymes in Control of Innate Antiviral Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2002484. [PMID: 33511009 PMCID: PMC7816709 DOI: 10.1002/advs.202002484] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/09/2020] [Indexed: 05/11/2023]
Abstract
Innate antiviral immunity is the first line of host defense against invading viral pathogens. Immunity activation primarily relies on the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Viral proteins or nucleic acids mainly engage three classes of PRRs: Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), and DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS). These receptors initiate a series of signaling cascades that lead to the production of proinflammatory cytokines and type I interferon (IFN-I) in response to viral infection. This system requires precise regulation to avoid aberrant activation. Emerging evidence has unveiled the crucial roles that the ubiquitin system, especially deubiquitinating enzymes (DUBs), play in controlling immune responses. In this review, an overview of the most current findings on the function of DUBs in the innate antiviral immune pathways is provided. Insights into the role of viral DUBs in counteracting host immune responses are also provided. Furthermore, the prospects and challenges of utilizing DUBs as therapeutic targets for infectious diseases are discussed.
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Affiliation(s)
- Zhi Zong
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Zhengkui Zhang
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
| | - Liming Wu
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
| | - Long Zhang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058P. R. China
| | - Fangfang Zhou
- Institute of Biology and Medical ScienceSoochow UniversitySuzhou215123P. R. China
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22
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Luo Z, Ang MJY, Chan SY, Yi Z, Goh YY, Yan S, Tao J, Liu K, Li X, Zhang H, Huang W, Liu X. Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community. RESEARCH (WASHINGTON, D.C.) 2020; 2020:6925296. [PMID: 32607499 PMCID: PMC7315394 DOI: 10.34133/2020/6925296] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 01/08/2023]
Abstract
The World Health Organization (WHO) has declared the outbreak of 2019 novel coronavirus, known as 2019-nCoV, a pandemic, as the coronavirus has now infected over 2.6 million people globally and caused more than 185,000 fatalities as of April 23, 2020. Coronavirus disease 2019 (COVID-19) causes a respiratory illness with symptoms such as dry cough, fever, sudden loss of smell, and, in more severe cases, difficulty breathing. To date, there is no specific vaccine or treatment proven effective against this viral disease. Early and accurate diagnosis of COVID-19 is thus critical to curbing its spread and improving health outcomes. Reverse transcription-polymerase chain reaction (RT-PCR) is commonly used to detect the presence of COVID-19. Other techniques, such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and microfluidics, have allowed better disease diagnosis. Here, as part of the effort to expand screening capacity, we review advances and challenges in the rapid detection of COVID-19 by targeting nucleic acids, antigens, or antibodies. We also summarize potential treatments and vaccines against COVID-19 and discuss ongoing clinical trials of interventions to reduce viral progression.
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Affiliation(s)
- Zichao Luo
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Melgious Jin Yan Ang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Siew Yin Chan
- Frontiers Science Center for Flexible Electronics & Shaanxi Institute of Flexible Electronics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zhigao Yi
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Yi Yiing Goh
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Shuangqian Yan
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Jun Tao
- Sports Medical Centre, The Second Affiliated Hospital of Nanchang University, Nanchang 330000, China
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Chang Chun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xiaosong Li
- Department of Oncology, The Fourth Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100048, China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Chang Chun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics & Shaanxi Institute of Flexible Electronics, Northwestern Polytechnical University, Xi'an 710072, China
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- The N.1 Institute for Health, National University of Singapore, Singapore
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Fuzhou 350807, China
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Tahir ul Qamar M, Bari A, Adeel MM, Maryam A, Ashfaq UA, Du X, Muneer I, Ahmad HI, Wang J. Peptide vaccine against chikungunya virus: immuno-informatics combined with molecular docking approach. J Transl Med 2018; 16:298. [PMID: 30368237 PMCID: PMC6204282 DOI: 10.1186/s12967-018-1672-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV), causes massive outbreaks of chikungunya infection in several regions of Asia, Africa and Central/South America. Being positive sense RNA virus, CHIKV replication within the host resulting in its genome mutation and led to difficulties in creation of vaccine, drugs and treatment strategies. Vector control strategy has been a gold standard to combat spreading of CHIKV infection, but to eradicate a species from the face of earth is not an easy task. Therefore, alongside vector control, there is a dire need to prevent the infection through vaccine as well as through antiviral strategies. METHODS This study was designed to find out conserved B cell and T cell epitopes of CHIKV structural proteins through immuno-informatics and computational approaches, which may play an important role in evoking the immune responses against CHIKV. RESULTS Several conserved cytotoxic T-lymphocyte epitopes, linear and conformational B cell epitopes were predicted for CHIKV structural polyprotein and their antigenicity was calculated. Among B-cell epitopes "PPFGAGRPGQFGDI" showed a high antigenicity score and it may be highly immunogenic. In case of T cell epitopes, MHC class I peptides 'TAECKDKNL' and MHC class II peptides 'VRYKCNCGG' were found extremely antigenic. CONCLUSION The study led to the discovery of various epitopes, conserved among various strains belonging to different countries. The potential antigenic epitopes can be successfully utilized in designing novel vaccines for combating and eradication of CHIKV disease.
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Affiliation(s)
- Muhammad Tahir ul Qamar
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University (HZAU), Wuhan, People’s Republic of China
| | - Amna Bari
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Muzammal Adeel
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University (HZAU), Wuhan, People’s Republic of China
| | - Arooma Maryam
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Islamabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Xiaoyong Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University (HZAU), Wuhan, People’s Republic of China
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Iqra Muneer
- School of Life Sciences, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Hafiz Ishfaq Ahmad
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Jia Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University (HZAU), Wuhan, People’s Republic of China
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, People’s Republic of China
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Pérez-Laguna V, García-Malinis AJ, Aspiroz C, Rezusta A, Gilaberte Y. Antimicrobial effects of photodynamic therapy. GIORN ITAL DERMAT V 2018; 153:833-846. [PMID: 29683289 DOI: 10.23736/s0392-0488.18.06007-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The microorganisms that cause infections are increasing their resistance to antibiotics. In this context, alternative treatments are necessary. The antimicrobial photodynamic therapy (aPDT) is a therapeutic modality based on photosensitizing molecules that end up generating reactive oxygen species that induce the destruction of the target cells when are irradiated with light of a suitable wavelength and at a proper dose. The cells targeted by aPDT are all types of microorganisms (bacteria, fungi and parasites) including viruses and has been proven effective against representative members of all of them. In the field of dermatology, aPDT has been tested with promising results in different infections such as chronic ulcers, acne, onychomycosis and other cutaneous mycoses, as well as in leishmaniasis. Therefore, it is presented as a possible treatment option against the agents that cause skin and/or mucous infections.
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Affiliation(s)
| | | | - Carmen Aspiroz
- Unit of Microbiology, Hospital Royo Villanova, Zaragoza, Spain
| | - Antonio Rezusta
- IIS Aragón, Zaragoza, Spain.,Department of Microbiology, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Yolanda Gilaberte
- IIS Aragón, Zaragoza, Spain - .,Department of Dermatology, Hospital Universitario Miguel Servet, Zaragoza, Spain
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Ahola T, Couderc T, Courderc T, Ng LFP, Hallengärd D, Powers A, Lecuit M, Esteban M, Merits A, Roques P, Liljeström P. Therapeutics and vaccines against chikungunya virus. Vector Borne Zoonotic Dis 2016; 15:250-7. [PMID: 25897811 DOI: 10.1089/vbz.2014.1681] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Currently, there are no licensed vaccines or therapies available against chikungunya virus (CHIKV), and these were subjects discussed during a CHIKV meeting recently organized in Langkawi, Malaysia. In this review, we chart the approaches taken in both areas. Because of a sharp increase in new data in these fields, the present paper is complementary to previous reviews by Weaver et al. in 2012 and Kaur and Chu in 2013 . The most promising antivirals so far discovered are reviewed, with a special focus on the virus-encoded replication proteins as potential targets. Within the vaccines in development, our review emphasizes the various strategies in parallel development that are unique in the vaccine field against a single disease.
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Affiliation(s)
- Tero Ahola
- 1 Department of Food and Environmental Sciences, University of Helsinki , Helsinki, Finland
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26
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Han C, Yang C. Viral plaque analysis on a wide field-of-view, time-lapse, on-chip imaging platform. Analyst 2015; 139:3727-34. [PMID: 24611157 DOI: 10.1039/c3an02323k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The observation of viral plaques is the standard method for determining the viral titer and understanding the behaviors of viruses. Here, we report the application of a wide field-of-view (FOV), time-lapse, on-chip imaging platform, termed the ePetri, for plaque analysis of murine norovirus 1 (MNV-1). The ePetri offers the ability to dynamically track plaques at the individual cell death event level over a wide FOV of 6 mm × 4 mm. As demonstration, we captured high-resolution time-lapse images of MNV-1-infected cells at 30 min intervals. We implemented a customized image-processing program containing a density-based clustering algorithm to analyze the spatial-temporal distribution of cell death events to identify plaques at their earliest stages. By using the results in a viral titer count format, we showed that our approach gives results that are comparable to conventional plaque assays. We further showed that the extra information collected by the ePetri can be used to monitor the dynamics of plaque formation and growth. Finally, we performed a demonstration experiment to show the relevance of such an experimental format for viral inhibitor study. We believe the ePetri is a simple and compact solution for the automation of viral plaque assays, plaque behavior analysis, and antiviral drug discovery and study.
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Affiliation(s)
- Chao Han
- Electrical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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27
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Ahola T, Karlin DG. Sequence analysis reveals a conserved extension in the capping enzyme of the alphavirus supergroup, and a homologous domain in nodaviruses. Biol Direct 2015; 10:16. [PMID: 25886938 PMCID: PMC4392871 DOI: 10.1186/s13062-015-0050-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/24/2015] [Indexed: 12/16/2022] Open
Abstract
Background Members of the alphavirus supergroup include human pathogens such as chikungunya virus, hepatitis E virus and rubella virus. They encode a capping enzyme with methyltransferase-guanylyltransferase (MTase-GTase) activity, which is an attractive drug target owing to its unique mechanism. However, its experimental study has proven very difficult. Results We examined over 50 genera of viruses by sequence analyses. Earlier studies showed that the MTase-GTase contains a “Core” region conserved in sequence. We show that it is followed by a long extension, which we termed “Iceberg” region, whose secondary structure, but not sequence, is strikingly conserved throughout the alphavirus supergroup. Sequence analyses strongly suggest that the minimal capping domain corresponds to the Core and Iceberg regions combined, which is supported by earlier experimental data. The Iceberg region contains all known membrane association sites that contribute to the assembly of viral replication factories. We predict that it may also contain an overlooked, widely conserved membrane-binding amphipathic helix. Unexpectedly, we detected a sequence homolog of the alphavirus MTase-GTase in taxa related to nodaviruses and to chronic bee paralysis virus. The presence of a capping enzyme in nodaviruses is biologically consistent, since they have capped genomes but replicate in the cytoplasm, where no cellular capping enzyme is present. The putative MTase-GTase domain of nodaviruses also contains membrane-binding sites that may drive the assembly of viral replication factories, revealing an unsuspected parallel with the alphavirus supergroup. Conclusions Our work will guide the functional analysis of the alphaviral MTase-GTase and the production of domains for structure determination. The identification of a homologous domain in a simple model system, nodaviruses, which replicate in numerous eukaryotic cell systems (yeast, flies, worms, mammals, and plants), can further help crack the function and structure of the enzyme. Reviewers This article was reviewed by Valerian Dolja, Eugene Koonin and Sebastian Maurer-Stroh. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0050-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tero Ahola
- Department of Food and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| | - David G Karlin
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK. .,The Division of Structural Biology, Henry Wellcome Building, Roosevelt Drive, Oxford, OX3 7BN, UK.
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de Lourdes G. Ferreira M, Pinheiro LCS, Santos-Filho OA, Peçanha MDS, Sacramento CQ, Machado V, Ferreira VF, Souza TML, Boechat N. Design, synthesis, and antiviral activity of new 1H-1,2,3-triazole nucleoside ribavirin analogs. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0762-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Shan Y, Zheng Y, Guan F, Zhou J, Zhao H, Xia B, Feng X. Purification and characterization of a novel anti-HSV-2 protein with antiproliferative and peroxidase activities from Stellaria media. Acta Biochim Biophys Sin (Shanghai) 2013; 45:649-55. [PMID: 23761431 DOI: 10.1093/abbs/gmt060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A novel antiviral protein, designated as Stellarmedin A, was purified from Stellaria media (L.) Vill. (Caryophyllaceae) by using ammonium sulfate precipitation, cation-exchange chromatography system. Gel electrophoresis analysis showed that Stellarmedin A is a highly basic glycoprotein with a molecular weight of 35.1 kDa and an isoelectric point of ∼8.7. The N-terminal 14-amino acid sequence, MGNTGVLTGERNDR, is similar to those of other plant peroxidases. This protein inhibited herpes simplex virus type 2 (HSV-2) replication in vitro with an IC50 of 13.18 µg/ml and a therapeutic index exceeding 75.9. It was demonstrated that Stellarmedin A affects the initial stage of HSV-2 infection and is able to inhibit the proliferation of promyelocytic leukemia HL-60 and colon carcinoma LoVo cells with an IC50 of 9.09 and 12.32 µM, respectively. Moreover, Stellarmedin A has a peroxidase activity of 36.6 µmol/min/mg protein, when guaiacol was used as substrate. To our knowledge, this is the first report about an anti-HSV-2 protein with antiproliferative and peroxidase activities from S. media.
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Affiliation(s)
- Yu Shan
- Jiangsu Center for Research & Development of Medicinal Plants, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden, Mem. Sun Yat-sen), Nanjing 210014, China
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30
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Das P, Deng X, Zhang L, Roth MG, Fontoura BMA, Phillips MA, De Brabander JK. SAR Based Optimization of a 4-Quinoline Carboxylic Acid Analog with Potent Anti-Viral Activity. ACS Med Chem Lett 2013; 4:517-521. [PMID: 23930152 DOI: 10.1021/ml300464h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
It is established that drugs targeting viral proteins are at risk of generating resistant strains. However, drugs targeting host factors can potentially avoid this problem. Herein we report structure-activity relationship studies leading to the discovery of a very potent lead compound 6-fluoro-2-(5-isopropyl-2-methyl-4-phenoxyphenyl)quinoline-4-carboxylic acid (C44) that inhibits human dihydroorotate dehydrogenase (DHODH) with an IC50 of 1 nM, and viral replication of VSV and WSN-Influenza with an EC50 of 2 nM and 41 nM. We also solved the X-ray structure of human DHODH bound to C44, providing structural insight into the potent inhibition of biaryl ether analogs of brequinar.
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Affiliation(s)
- Priyabrata Das
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Xiaoyi Deng
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Liang Zhang
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Michael G. Roth
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Beatriz M. A. Fontoura
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Margaret A. Phillips
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Jef K. De Brabander
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
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31
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Betts RJ, Mann TS, Henry PJ. Inhibitory influence of the hexapeptidic sequence SLIGRL on influenza A virus infection in mice. J Pharmacol Exp Ther 2012; 343:725-35. [PMID: 22988062 DOI: 10.1124/jpet.112.196485] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Proteinase-activated receptor 2 (PAR(2)) is widely expressed in the respiratory tract and is an integral component of the host antimicrobial defense system. The principal aim of this study was to investigate the influence of a PAR(2)-activating peptide, SLIGRL, on influenza A virus (IAV)-induced pathogenesis in mice. Intranasal inoculation of BALB/c mice with influenza A/PR/8/34 virus caused time-dependent increases in the number of pulmonary leukocytes (recovered from bronchoalveolar lavage fluid), marked airway histopathology characterized by extensive epithelial cell damage, airway hyper-responsiveness to the bronchoconstrictor methacholine, and elevated levels of inflammatory chemokines (keratinocyte-derived chemokine and macrophage inflammatory protein 2) and cytokines (interferon-γ). It is noteworthy that these IAV-induced effects were dose-dependently attenuated in mice treated with a PAR(2)-activating peptide, SLIGRL, at the time of IAV inoculation. However, SLIGRL also inhibited IAV-induced increases in pulmonary leukocytes in PAR(2)-deficient mice, indicating these antiviral actions were not mediated by PAR(2). The potency order obtained for a series of structural analogs of SLIGRL for anti-IAV activity (IGRL > SLIGRL > LSIGRL >2-furoyl-LIGRL) was also inconsistent with a PAR(2)-mediated effect. In further mechanistic studies, SLIGRL inhibited IAV-induced propagation in ex vivo perfused segments of trachea from wild-type or PAR(2)(-/-) mice, but did not inhibit viral attachment or replication in Madin-Darby canine kidney cells and chorioallantoic membrane cells, which are established hosts for IAV. In summary, SLIGRL protected mice from IAV infection independently of PAR(2) and independently of direct inhibition of IAV attachment or replication, potentially through the activation of endogenous antiviral pathways within the mouse respiratory tract.
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Affiliation(s)
- Richard J Betts
- School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia
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Hussain Basha S, Prasad RN. In-Silico screening of Pleconaril and its novel substituted derivatives with Neuraminidase of H1N1 Influenza strain. BMC Res Notes 2012; 5:105. [PMID: 22340192 PMCID: PMC3369820 DOI: 10.1186/1756-0500-5-105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/17/2012] [Indexed: 11/10/2022] Open
Abstract
Background Neuraminidase (NA) is a prominent surface antigen of Influenza viruses, which helps in release of viruses from the host cells after replication. Anti influenza drugs such as Oseltamivir target a highly conserved active site of NA, which comprises of 8 functional residues (R118, D151, R152, R224, E276, R292, R371 and Y406) to restrict viral release from host cells, thus inhibiting its ability to cleave sialic acid residues on the cell membrane. Reports on the emergence of Oseltamivir resistant strains of H1N1 Influenza virus necessitated a search for alternative drug candidates. Pleconaril is a novel antiviral drug being developed by Schering-Plough to treat Picornaviridae infections, and is in its late clinical trials stage. Since, Pleconaril was designed to bind the highly conserved hydrophobic binding site on VP1 protein of Picorna viruses, the ability of Pleconaril and its novel substituted derivatives to bind highly conserved hydrophobic active site of H1N1 Neuraminidase, targeting which oseltamivir has been designed was investigated. Result 310 novel substituted variants of Pleconaril were designed using Chemsketch software and docked into the highly conserved active site of NA using arguslab software. 198 out of 310 Pleconaril variants analyzed for docking with NA active site were proven effective, based on their free binding energy. Conclusion Pleconaril variants with F, Cl, Br, CH3, OH and aromatic ring substitutions were shown to be effective alternatives to Oseltamivir as anti influenza drugs.
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Affiliation(s)
- Syed Hussain Basha
- Dept. of Biotechnology, REVA Institute of Science and Management, Yelahanka, Bangalore 560064, India.
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Decroly E, Ferron F, Lescar J, Canard B. Conventional and unconventional mechanisms for capping viral mRNA. Nat Rev Microbiol 2011; 10:51-65. [PMID: 22138959 PMCID: PMC7097100 DOI: 10.1038/nrmicro2675] [Citation(s) in RCA: 338] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNAs are protected at their 5′ ends by a cap structure consisting of an N7-methylated GTP molecule linked to the first transcribed nucleotide by a 5′–5′ triphosphate bond. The cap structure is essential for RNA splicing, export and stability, and allows the ribosomal complex to recognize mRNAs and ensure their efficient translation. Uncapped RNA molecules are degraded in cytoplasmic granular compartments called processing bodies and may be detected as 'non-self' by the host cell, triggering antiviral innate immune responses through the production of interferons. Conventional RNA capping (that is, of mRNAs from the host cell and from DNA viruses) requires hydrolysis of the 5′ γ-phosphate of RNA by an RNA triphosphatase, transfer of a GMP molecule onto the 5′-end of RNA by a guanylyltransferase, and methylation of this guanosine by an (guanine-N7)-methyltransferase. Subsequent methylations on the first and second transcribed nucleotides by (nucleoside-2′-O)-methyltransferases form cap-1 and cap-2 structures. Viruses have evolved highly diverse capping mechanisms to acquire cap structures using their own or cellular capping machineries, or by stealing cap structures from cellular mRNAs. Virally encoded RNA-capping machineries are diverse in terms of their genetic components, protein domain organization, enzyme structures, and reaction mechanisms and pathways, making viral RNA capping an attractive target for antiviral-drug design.
Capping the 5′ end of eukaryotic mRNAs with a 7-methylguanosine moiety enables efficient splicing, nuclear export and translation of mRNAs, and also limits their degradation by cellular exonucleases. Here, Canard and colleagues describe how viruses synthesize their own mRNA cap structures or steal them from host mRNAs, allowing efficient synthesis of viral proteins and avoidance of host innate immune responses. In the eukaryotic cell, capping of mRNA 5′ ends is an essential structural modification that allows efficient mRNA translation, directs pre-mRNA splicing and mRNA export from the nucleus, limits mRNA degradation by cellular 5′–3′ exonucleases and allows recognition of foreign RNAs (including viral transcripts) as 'non-self'. However, viruses have evolved mechanisms to protect their RNA 5′ ends with either a covalently attached peptide or a cap moiety (7-methyl-Gppp, in which p is a phosphate group) that is indistinguishable from cellular mRNA cap structures. Viral RNA caps can be stolen from cellular mRNAs or synthesized using either a host- or virus-encoded capping apparatus, and these capping assemblies exhibit a wide diversity in organization, structure and mechanism. Here, we review the strategies used by viruses of eukaryotic cells to produce functional mRNA 5′-caps and escape innate immunity.
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Affiliation(s)
- Etienne Decroly
- Centre National de Recherche Scientifique and Aix-Marseille Université, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288 Marseille cedex 09, France
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Dhanachandra Singh K, Kirubakaran P, Manikandaprabhu S, Nagamani S, Srinivasan P, Karthikeyan M. Docking Studies of Adenosine Analogues with NS5 Methyltransferase of Yellow Fever Virus. Indian J Microbiol 2011; 52:28-34. [PMID: 23449064 DOI: 10.1007/s12088-011-0201-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 09/27/2010] [Indexed: 12/31/2022] Open
Abstract
Yellow fever virus (YFV) is caused by single stranded positive RNA virus called Flavivirus. Till now no specific antiviral agents are available for the treatment of YFV, and despite a commercial YFV vaccine, there are still approximately 30,000 deaths worldwide each year and cases have been increasing in the last 20 years. Here, the effects of adenosine analogues and commercially available adenosine derivative drugs on NS5 methyltransferase of YFV have been performed by the comparative docking study. Based on the docking score, the glide energy and the number of interactions of the adenosine analogues with the Pubchem ID 13792 and 1077 showed the better scoring function than the best ranked commercially available adenosine analogue derived antiviral drug Cc3ado. From the docking result it reveals that these adenosine analogues can bind to the active site of NS5 methyltransferase protein and inhibit the viral replication.
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Affiliation(s)
- Kh Dhanachandra Singh
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamilnadu 630 003 India
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Pohjala L, Alakurtti S, Ahola T, Yli-Kauhaluoma J, Tammela P. Betulin-derived compounds as inhibitors of alphavirus replication. JOURNAL OF NATURAL PRODUCTS 2009; 72:1917-1926. [PMID: 19839605 DOI: 10.1021/np9003245] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper describes inhibition of Semliki Forest virus (SFV) replication by synthetic derivatives of naturally occurring triterpenoid betulin (1). Chemical modifications were made to OH groups at C-3 and C-28 and to the C-20-C-29 double bond. A set of heterocyclic betulin derivatives was also assayed. A free or acetylated OH group at C-3 was identified as an important structural contributor for anti-SFV activity, 3,28-di-O-acetylbetulin (4) being the most potent derivative (IC50 value 9.1 microM). Betulinic acid (13), 28-O-tetrahydropyranylbetulin (17), and a triazolidine derivative (41) were also shown to inhibit Sindbis virus, with IC50 values of 0.5, 1.9, and 6.1 microM, respectively. The latter three compounds also had significant synergistic effects against SFV when combined with 3'-amino-3'-deoxyadenosine. In contrast to previous work on other viruses, the antiviral activity of 13 was mapped to take place in virus replication phase. The efficacy was also shown to be independent of external guanosine supplementation.
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Affiliation(s)
- Leena Pohjala
- Centre for Drug Research, Faculty of Pharmacy, P.O. Box 56, FI-00014 University of Helsinki, Finland
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Determinants of RNA-dependent RNA polymerase (in)fidelity revealed by kinetic analysis of the polymerase encoded by a foot-and-mouth disease virus mutant with reduced sensitivity to ribavirin. J Virol 2008; 82:12346-55. [PMID: 18829745 DOI: 10.1128/jvi.01297-08] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A mutant poliovirus (PV) encoding a change in its polymerase (3Dpol) at a site remote from the catalytic center (G64S) confers reduced sensitivity to ribavirin and forms a restricted quasispecies, because G64S 3Dpol is a high-fidelity enzyme. A foot-and-mouth disease virus (FMDV) mutant that encodes a change in the polymerase catalytic site (M296I) exhibits reduced sensitivity to ribavirin without restricting the viral quasispecies. In order to resolve this apparent paradox, we have established a minimal kinetic mechanism for nucleotide addition by wild-type (WT) FMDV 3Dpol that permits a direct comparison to PV 3Dpol as well as to FMDV 3Dpol derivatives. Rate constants for correct nucleotide addition were on par with those of PV 3Dpol, but apparent binding constants for correct nucleotides were higher than those observed for PV 3Dpol. The A-to-G transition frequency was calculated to be 1/20,000, which is quite similar to that calculated for PV 3Dpol. The analysis of FMDV M296I 3Dpol revealed a decrease in the calculated ribavirin incorporation frequency (1/8,000) relative to that (1/4,000) observed for the WT enzyme. Unexpectedly, the A-to-G transition frequency was higher (1/8,000) than that observed for the WT enzyme. Therefore, FMDV selected a polymerase that increases the frequency of the misincorporation of natural nucleotides while specifically decreasing the frequency of the incorporation of ribavirin nucleotide. These studies provide a mechanistic framework for understanding FMDV 3Dpol structure-function relationships, provide the first direct analysis of the fidelity of FMDV 3Dpol in vitro, identify the beta9-alpha11 loop as a (in)fidelity determinant, and demonstrate that not all ribavirin-resistant mutants will encode high-fidelity polymerases.
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A morpholino oligomer targeting highly conserved internal ribosome entry site sequence is able to inhibit multiple species of picornavirus. Antimicrob Agents Chemother 2008; 52:1970-81. [PMID: 18347107 DOI: 10.1128/aac.00011-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the genera Enterovirus and Rhinovirus (family Picornaviridae) cause a wide range of human diseases. An established vaccine is available only for poliovirus, and no effective therapy is available for the treatment of infections caused by any pathogenic picornavirus. Peptide-conjugated phosphorodiamidate morpholino oligomers (PPMO) are single-stranded DNA-like antisense agents that readily enter cells. A panel of PPMO was tested for their antiviral activities against various picornaviruses. PPMO targeting conserved internal ribosome entry site (IRES) sequence were highly active against human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1), reducing PV1 titers by up to 6 log(10) in cell cultures. Comparative sequence analysis led us to design a PPMO (EnteroX) targeting 22 nucleotides of IRES sequence that are perfectly conserved across greater than 99% of all human enteroviruses and rhinoviruses. EnteroX reduced PV1 replication in cell culture to an extent similar to that of other IRES-specific PPMO. Resistant PV1 arose in cell cultures after 12 passages in the presence of EnteroX and were found to have two mutations within the EnteroX target sequence. Nevertheless, cPVR transgenic mice treated once daily by intraperitoneal (i.p.) injection with EnteroX before and/or after i.p. infection with 3 x 10(8) PFU (three times the 50% lethal dose) of PV1 had an approximately 80% higher rate of survival than the controls. The viral titer in tissues taken at day 5 postinfection showed that animals in the EnteroX-treated group averaged over 3, 4, and 5 log(10) less virus in the small intestine, spinal cord, and brain, respectively, than the amount in the control animals. These results suggest that EnteroX may have broad therapeutic potential against entero- and rhinoviruses.
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Egloff MP, Decroly E, Malet H, Selisko B, Benarroch D, Ferron F, Canard B. Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5. J Mol Biol 2007; 372:723-36. [PMID: 17686489 DOI: 10.1016/j.jmb.2007.07.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 07/02/2007] [Accepted: 07/05/2007] [Indexed: 11/27/2022]
Abstract
The N-terminal 33 kDa domain of non-structural protein 5 (NS5) of dengue virus (DV), named NS5MTase(DV), is involved in two of four steps required for the formation of the viral mRNA cap (7Me)GpppA(2'OMe), the guanine-N7 and the adenosine-2'O methylation. Its S-adenosyl-l-methionine (AdoMet) dependent 2'O-methyltransferase (MTase) activity has been shown on capped (7Me+/-)GpppAC(n) RNAs. Here we report structural and binding studies using cap analogues and capped RNAs. We have solved five crystal structures at 1.8 A to 2.8 A resolution of NS5MTase(DV) in complex with cap analogues and the co-product of methylation S-adenosyl-l-homocysteine (AdoHcy). The cap analogues can adopt several conformations. The guanosine moiety of all cap analogues occupies a GTP-binding site identified earlier, indicating that GTP and cap share the same binding site. Accordingly, we show that binding of (7Me)GpppAC(4) and (7Me)GpppAC(5) RNAs is inhibited in the presence of GTP, (7Me)GTP and (7Me)GpppA but not by ATP. This particular position of the cap is in accordance with the 2'O-methylation step. A model was generated of a ternary 2'O-methylation complex of NS5MTase(DV), (7Me)GpppA and AdoMet. RNA-binding increased when (7Me+/-)GpppAGC(n-1) starting with the consensus sequence GpppAG, was used instead of (7Me+/-)GpppAC(n). In the NS5MTase(DV)-GpppA complex the cap analogue adopts a folded, stacked conformation uniquely possible when adenine is the first transcribed nucleotide at the 5' end of nascent RNA, as it is the case in all flaviviruses. This conformation cannot be a functional intermediate of methylation, since both the guanine-N7 and adenosine-2'O positions are too far away from AdoMet. We hypothesize that this conformation mimics the reaction product of a yet-to-be-demonstrated guanylyltransferase activity. A putative Flavivirus RNA capping pathway is proposed combining the different steps where the NS5MTase domain is involved.
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Affiliation(s)
- Marie-Pierre Egloff
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, 13288 Marseille, France
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Lulla A, Lulla V, Tints K, Ahola T, Merits A. Molecular determinants of substrate specificity for Semliki Forest virus nonstructural protease. J Virol 2007; 80:5413-22. [PMID: 16699022 PMCID: PMC1472149 DOI: 10.1128/jvi.00229-06] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C-terminal cysteine protease domain of Semliki Forest virus nonstructural protein 2 (nsP2) regulates the virus life cycle by sequentially cleaving at three specific sites within the virus-encoded replicase polyprotein P1234. The site between nsP3 and nsP4 (the 3/4 site) is cleaved most efficiently. Analysis of Semliki Forest virus-specific cleavage sites with shuffled N-terminal and C-terminal half-sites showed that the main determinants of cleavage efficiency are located in the region preceding the cleavage site. Random mutagenesis analysis revealed that amino acid residues in positions P4, P3, P2, and P1 of the 3/4 cleavage site cannot tolerate much variation, whereas in the P5 position most residues were permitted. When mutations affecting cleavage efficiency were introduced into the 2/3 and 3/4 cleavage sites, the resulting viruses remained viable but had similar defects in P1234 processing as observed in the in vitro assay. Complete blockage of the 3/4 cleavage was found to be lethal. The amino acid in position P1' had a significant effect on cleavage efficiency, and in this regard the protease markedly preferred a glycine residue over the tyrosine natively present in the 3/4 site. Therefore, the cleavage sites represent a compromise between protease recognition and other requirements of the virus life cycle. The protease recognizes at least residues P4 to P1', and the P4 arginine residue plays an important role in the fast cleavage of the 3/4 site.
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Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. Genome-wide diversity and selective pressure in the human rhinovirus. Virol J 2007; 4:40. [PMID: 17477878 PMCID: PMC1892812 DOI: 10.1186/1743-422x-4-40] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Accepted: 05/03/2007] [Indexed: 01/19/2023] Open
Abstract
Background The human rhinoviruses (HRV) are one of the most common and diverse respiratory pathogens of humans. Over 100 distinct HRV serotypes are known, yet only 6 genomes are available. Due to the paucity of HRV genome sequence, little is known about the genetic diversity within HRV or the forces driving this diversity. Previous comparative genome sequence analyses indicate that recombination drives diversification in multiple genera of the picornavirus family, yet it remains unclear if this holds for HRV. Results To resolve this and gain insight into the forces driving diversification in HRV, we generated a representative set of 34 fully sequenced HRVs. Analysis of these genomes shows consistent phylogenies across the genome, conserved non-coding elements, and only limited recombination. However, spikes of genetic diversity at both the nucleotide and amino acid level are detectable within every locus of the genome. Despite this, the HRV genome as a whole is under purifying selective pressure, with islands of diversifying pressure in the VP1, VP2, and VP3 structural genes and two non-structural genes, the 3C protease and 3D polymerase. Mapping diversifying residues in these factors onto available 3-dimensional structures revealed the diversifying capsid residues partition to the external surface of the viral particle in statistically significant proximity to antigenic sites. Diversifying pressure in the pleconaril binding site is confined to a single residue known to confer drug resistance (VP1 191). In contrast, diversifying pressure in the non-structural genes is less clear, mapping both nearby and beyond characterized functional domains of these factors. Conclusion This work provides a foundation for understanding HRV genetic diversity and insight into the underlying biology driving evolution in HRV. It expands our knowledge of the genome sequence space that HRV reference serotypes occupy and how the pattern of genetic diversity across HRV genomes differs from other picornaviruses. It also reveals evidence of diversifying selective pressure in both structural genes known to interact with the host immune system and in domains of unassigned function in the non-structural 3C and 3D genes, raising the possibility that diversification of undiscovered functions in these essential factors may influence HRV fitness and evolution.
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Affiliation(s)
- Amy L Kistler
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Howard Hughes Medical Institute, University of California, California, USA
| | - Dale R Webster
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Biological and Medical Informatics Program, University of California, San Francisco, California, USA
- Howard Hughes Medical Institute, University of California, California, USA
| | - Silvi Rouskin
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Howard Hughes Medical Institute, University of California, California, USA
| | - Vince Magrini
- Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Joel J Credle
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Howard Hughes Medical Institute, University of California, California, USA
| | - David P Schnurr
- California Department of Health Services, Richmond, California, USA
| | - Homer A Boushey
- Department of Medicine, University of California, San Francisco, California, USA
| | - Elaine R Mardis
- Department of Genetics, Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Howard Hughes Medical Institute, University of California, California, USA
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He Y, Duan W, Tan SL. Emerging host cell targets for hepatitis C therapy. Drug Discov Today 2007; 12:209-17. [PMID: 17331885 DOI: 10.1016/j.drudis.2007.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 01/03/2007] [Accepted: 01/24/2007] [Indexed: 12/23/2022]
Abstract
Chronic hepatitis C virus (HCV) infection is a major burden on humanity. The current HCV therapy has limited efficacy, and there is pressing need for new and more effective therapies. Host cell factors that are required for HCV infection, replication and/or pathogenesis represent potential therapeutic targets. Of particular interest are cellular receptors that mediate HCV entry, factors that facilitate HCV replication and assembly, and intracellular pathways involving lipid biosynthesis, oxidative stress and innate immune response. A crucial challenge now is to manipulate such cellular targets pharmacologically for chronic HCV treatment, without being limited by side effects.
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Affiliation(s)
- Yupeng He
- Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA.
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Zhou L, Thakur CS, Molinaro RJ, Paranjape JM, Hoppes R, Jeang KT, Silverman RH, Torrence PF. Delivery of 2-5A cargo into living cells using the Tat cell penetrating peptide: 2-5A-tat. Bioorg Med Chem 2007; 14:7862-74. [PMID: 16908165 DOI: 10.1016/j.bmc.2006.07.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Accepted: 07/27/2006] [Indexed: 11/22/2022]
Abstract
2',5'-Oligoadenylate tetramer (2-5A) has been chemically conjugated to short HIV-1 Tat peptides to provide 2-5A-tat chimeras. Two different convergent synthetic approaches have been employed to provide such 2-5A-tat bioconjugates. One involved generation of a bioconjugate through reaction of a cysteine terminated Tat peptide with a alpha-chloroacetyl derivative of 2-5A. The second synthetic strategy was based upon a cycloaddition reaction of an azide derivative of 2-5A with a Tat peptide bearing an alkyne function. Either bioconjugate of 2-5A-tat was able to activate human RNase L. The union of 2-5A and Tat peptide provided an RNase L-active chimeric nucleopeptide with the ability to be taken up by cells by virtue of the Tat peptide and to activate RNase L in intact cells. This strategy provides a valuable vehicle for the entry of the charged 2-5A molecule into cells and may provide a means for targeted destruction of HIV RNA in vivo.
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Affiliation(s)
- Longhu Zhou
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA
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Vyas TK, Shah L, Amiji MM. Nanoparticulate drug carriers for delivery of HIV/AIDS therapy to viral reservoir sites. Expert Opin Drug Deliv 2006; 3:613-28. [PMID: 16948557 DOI: 10.1517/17425247.3.5.613] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Providing the optimum treatment of AIDS is a major challenge in the 21st Century. HIV is localised and harboured in certain inaccessible compartments of the body, such as the CNS, the cerebrospinal fluid, the lymphatic system and in the macrophages, where it cannot be reached by the majority of therapeutic agents in adequate concentrations or in which the therapeutic agents cannot reside for the necessary duration. Progression in HIV/AIDS treatment suggests that available therapy can lower the systemic viral load below the detection limit. However, on discontinuation of treatment, there is relapse of the infection from the reservoir sites and a potential for resistance development. This review discusses the aetiology and pathology of HIV, with emphasis on the viral reservoirs, current therapy of AIDS, and the opportunity for nanotechnology-based drug delivery systems to facilitate complete eradication of viral load from the reservoir sites. Literature-cited examples of drug delivery systems that are under investigation for the treatment of AIDS are discussed. The article also focuses on the future outlook and strategies for investigational drug formulations that use nanotherapeutic strategy for HIV/AIDS.
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Affiliation(s)
- Tushar K Vyas
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, 110 Mugar Life Sciences Building, Boston, MA 02115, USA
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Cattori V, Tandon R, Pepin A, Lutz H, Hofmann-Lehmann R. Rapid detection of feline leukemia virus provirus integration into feline genomic DNA. Mol Cell Probes 2006; 20:172-81. [PMID: 16488115 DOI: 10.1016/j.mcp.2005.11.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 11/18/2005] [Indexed: 01/21/2023]
Abstract
Feline leukemia virus (FeLV) is a gamma retrovirus that induces fatal diseases in domestic cats. Efficacious FeLV vaccines prevent persistent viremia and development of FeLV-related disease after virus exposure, but not minimal viral replication and a provirus-positive state as recently demonstrated using sensitive real-time PCR assays. Proviral integration is an important parameter of latent infection and persistence of retroviruses in infected cells. So far, FeLV-specific real-time PCR assays could not distinguish between the integrated and episomal forms of the provirus. Thus, it was the aim of the present study to develop a rapid assay for the detection of FeLV proviral integration. The test combines conventional and quantitative real-time PCR that use virus-specific primers and primers specific for cat genomic small interspersed nuclear elements. It was applied to analyze the time course of proviral integration into the genome of a feline fibroblast cell line and detect provirus integration in peripheral white blood cells from vaccinated and unvaccinated, FeLV-exposed cats. The newly developed rapid test will essentially contribute to a better understanding of the mechanisms involved in the pathogenesis of FeLV infection and be especially useful in the development of antiretroviral vaccines and therapies aimed at the inhibition of proviral integration.
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Affiliation(s)
- Valentino Cattori
- Clinical Laboratory, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, CH-8057 Zurich, Switzerland.
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Alves-Rodrigues I, Galão RP, Meyerhans A, Díez J. Saccharomyces cerevisiae: a useful model host to study fundamental biology of viral replication. Virus Res 2006; 120:49-56. [PMID: 16698107 PMCID: PMC7114155 DOI: 10.1016/j.virusres.2005.11.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 11/16/2005] [Accepted: 11/21/2005] [Indexed: 02/02/2023]
Abstract
Understanding the fundamental steps of virus life cycles including virus–host interactions is essential for the design of effective antiviral strategies. Such understanding has been deferred by the complexity of higher eukaryotic host organisms. To circumvent experimental difficulties associated with this, systems were developed to replicate viruses in the yeast Saccharomyces cerevisiae. The systems include viruses with RNA and DNA genomes that infect plants, animals and humans. By using the powerful methodologies available for yeast genetic analysis, fundamental processes occurring during virus replication have been brought to light. Here, we review the different viruses able to direct replication and gene expression in yeast and discuss their main contributions in the understanding of virus biology.
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Affiliation(s)
- Isabel Alves-Rodrigues
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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Abstract
During antiviral drug development, any essential stage of the viral life cycle can serve as a potential drug target. Since most viruses encode specific proteases whose cleavage activity is required for viral replication, and whose structure and activity are unique to the virus and not the host cell, these enzymes make excellent targets for drug development. Success using this approach has been demonstrated with the plethora of protease inhibitors approved for use against HIV. This discussion is designed to review the field of antiviral drug development, focusing on the search for protease inhibitors, while highlighting some of the challenges encountered along the way. Protease inhibitor drug discovery efforts highlighting progress made with HIV, HCV, HRV, and vaccinia virus as a model system are included. Drug Dev. Res. 67:501–510, 2006. © 2006 Wiley‐Liss, Inc.
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Affiliation(s)
| | - Dennis E. Hruby
- SIGA Technologies, Inc., Corvallis, Oregon
- Department of Microbiology, Oregon State University, Corvallis, Oregon
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