1
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Musatat AB, Durmuş T, Atahan A. Harnessing high potential benzothiazole chalcones against dengue virus NS5 protein: A multi-faceted theoretical study through molecular docking, ADME, and DFT. Arch Biochem Biophys 2024; 761:110171. [PMID: 39366630 DOI: 10.1016/j.abb.2024.110171] [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: 07/22/2024] [Revised: 09/13/2024] [Accepted: 09/30/2024] [Indexed: 10/06/2024]
Abstract
Chalcones bearing tetralone, indanone and benzothiazole cores were synthesized successfully using a general Claisen-Schmidt condensation protocol. The prepared compounds were purified and structurally analyzed by 1H, 13C NMR, and FT-IR techniques. A multi-faceted theoretical approach, combining Density Functional Theory (DFT), molecular docking, and ADME predictions, was employed to evaluate their therapeutic potential. DFT calculations at the B3LYP/def2-TZVP level revealed key electronic properties, with TD3 compound demonstrating the highest chemical reactivity. Molecular Electrostatic Potential (MEP) and Reduced Density Gradient (RDG) analyses provided insights into the compounds' non-covalent interactions and charge distributions. Molecular docking studies against the NS5 protein (PDB: 6KR2) showed superior binding affinities for all three compounds compared to the control ligand SAH, with TD3 exhibiting the lowest binding energy (-8.41 kcal/mol) and theoretical inhibition constant (689.31 nM). ADME predictions indicated favorable drug-like properties with concerns regarding aqueous solubility and potential P-glycoprotein interactions. Toxicity evaluations highlighted challenges, particularly in hepatotoxicity and carcinogenicity. The study identified TD3 as a promising lead compound for Dengue Virus NS5 inhibition, while also emphasizing the need for targeted modifications to address toxicity concerns. This research not only contributes to anti-dengue drug discovery efforts but also provides a robust methodological framework for the theoretical evaluation of similar small compounds in future investigations.
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Affiliation(s)
| | - Tülay Durmuş
- Department of Chemistry, Faculty of Art and Sciences, Düzce University, 81100, Düzce, Turkiye
| | - Alparslan Atahan
- Department of Chemistry, Faculty of Art and Sciences, Düzce University, 81100, Düzce, Turkiye
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2
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Imam MA, Alandijany TA, Felemban HR, Attar RM, Faizo AA, Gattan HS, Dwivedi VD, Azhar EI. Machine learning, network pharmacology, and molecular dynamics reveal potent cyclopeptide inhibitors against dengue virus proteins. Mol Divers 2024:10.1007/s11030-024-10975-w. [PMID: 39227512 DOI: 10.1007/s11030-024-10975-w] [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: 07/12/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
The dengue virus is a major global health hazard responsible for an estimated 390 million diseases yearly. This study focused on identifying cyclopeptide inhibitors for envelope structural proteins E, NS1, NS3, and NS5. Additionally, 5579 cyclopeptides were individually screened against the four target proteins using a machine learning-based quantitative structure-activity relationship model. Subsequently, the best 10 cyclopeptides from each protein were selected for molecular docking with their corresponding proteins. Moreover, the protein-peptide complexes with the highest affinity were subjected to a 100-ns molecular dynamics simulation. The protein-protein complexes exhibited superior structural stability and binding interactions. Based on the results of the MD simulation analyses, which included checking values for Root Mean Square Deviation, Root Mean Square Fluctuation, Principal Component Analysis (PCA), free energy landscapes, and energetic components, it was found that NS5-CP03714 complex is more stable and has stronger binding interactions than NS3-CP02054. PCA and free energy landscape plots have confirmed the higher conformational stability of NS5-CP03714. Analysis of the energetic components revealed that NS5-CP03714 (total binding energy = - 47.19 kcal/mol) exhibits more favorable interaction energies and overall binding energy compared to NS3-CP02054 (total binding energy = - 27.36 kcal/mol), suggesting a stronger and more stable formation of the complex. In addition, the drug-target network of two specific peptides (CP02950 and CP05582) and their associated target proteins were analyzed. This analysis revealed valuable information about their ability to target several proteins and their potential for broad-spectrum activity. Additional experimental investigations are necessary to validate these computational results and assess the efficacy of identified peptide inhibitors in biological systems.
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Affiliation(s)
- Mohammed A Imam
- Department of Medical Microbiology and Parasitology, Qunfudah Faculty of Medicine, Umm Al-Qura University, Al-Qunfudah, 21961, Saudi Arabia
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Thamir A Alandijany
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Hashim R Felemban
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Roba M Attar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Biological Sciences/Microbiology, Faculty of Science, University of Jeddah, , 21959, Jeddah, Saudi Arabia
| | - Arwa A Faizo
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Hattan S Gattan
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai, India.
- Bioinformatics Research Division, Quanta Calculus, Greater Noida, India.
| | - Esam I Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia.
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3
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Chauhan N, Gaur KK, Asuru TR, Guchhait P. Dengue virus: pathogenesis and potential for small molecule inhibitors. Biosci Rep 2024; 44:BSR20240134. [PMID: 39051974 PMCID: PMC11327219 DOI: 10.1042/bsr20240134] [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: 06/04/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 07/27/2024] Open
Abstract
Dengue, caused by dengue virus (DENV), is now endemic in nearly 100 countries and infection incidence is reported in another 30 countries. Yearly an estimated 400 million cases and 2200 deaths are reported. Effective vaccines against DENV are limited and there has been significant focus on the development of effective antiviral against the disease. The World Health Organization has initiated research programs to prioritize the development and optimization of antiviral agents against several viruses including Flaviviridae. A significant effort has been taken by the researchers to develop effective antivirals against DENV. Several potential small-molecule inhibitors like efavirenz, tipranavir and dasabuvir have been tested against envelope and non-structural proteins of DENV, and are in clinical trials around the world. We recently developed one small molecule, namely 7D, targeting the host PF4-CXCR3 axis. 7D inhibited all 4 serotypes of DENV in vitro and specifically DENV2 infection in two different mice models. Although the development of dengue vaccines remains a high priority, antibody cross reactivity among the serotypes and resulting antibody-dependent enhancement (ADE) of infection are major concerns that have limited the development of effective vaccine against DENV. Therefore, there has been a significant emphasis on the development of antiviral drugs against dengue. This review article describes the rescue effects of some of the small molecule inhibitors to viral/host factors associated with DENV pathogenesis.
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Affiliation(s)
- Navya Chauhan
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Kishan Kumar Gaur
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Tejeswara Rao Asuru
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Prasenjit Guchhait
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
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4
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Tseng AC, Nerurkar VR, Neupane KR, Kae H, Kaufusi PH. Membrane Retention of West Nile Virus NS5 Depends on NS1 or NS3 for Enzymatic Activity. Viruses 2024; 16:1303. [PMID: 39205277 PMCID: PMC11360346 DOI: 10.3390/v16081303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 08/10/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
West Nile virus (WNV) nonstructural protein 5 (NS5) possesses multiple enzymatic domains essential for viral RNA replication. During infection, NS5 predominantly localizes to unique replication organelles (ROs) at the rough endoplasmic reticulum (RER), known as vesicle packets (VPs) and convoluted membranes (CMs), with a portion of NS5 accumulating in the nucleus. NS5 is a soluble protein that must be in the VP, where its enzymatic activities are required for viral RNA synthesis. However, the mechanistic processes behind the recruitment of NS5 from the cytoplasm to the RER membrane remain unclear. Here, we utilize high-resolution confocal microscopy and sucrose density gradient ultracentrifugation to investigate whether the association of NS5 with other NS proteins contributes to its membrane recruitment and retention. We demonstrate that NS1 or NS3 partially influences the NS5 association with the membrane. We further demonstrate that processed NS5 is predominantly in the cytoplasm and nucleus, indicating that the processing of NS5 from the viral polyprotein does not contribute to its membrane localization. These observations suggest that other host or viral factors, such as the enwrapment of NS5 by the RO, may also be necessary for the complete membrane retention of NS5. Therefore, studies on the inhibitors that disrupt the membrane localization of WNV NS5 are warranted for antiviral drug development.
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Affiliation(s)
- Alanna C. Tseng
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA;
- Molecular Biosciences and Bioengineering Graduate Program, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Vivek R. Nerurkar
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA;
- Molecular Biosciences and Bioengineering Graduate Program, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Kabi R. Neupane
- Division of Math and Sciences, Leeward Community College, Pearl City, HI 96782, USA; (K.R.N.); (H.K.)
| | - Helmut Kae
- Division of Math and Sciences, Leeward Community College, Pearl City, HI 96782, USA; (K.R.N.); (H.K.)
| | - Pakieli H. Kaufusi
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA;
- Molecular Biosciences and Bioengineering Graduate Program, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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5
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Krejčová K, Krafcikova P, Klima M, Chalupska D, Chalupsky K, Zilecka E, Boura E. Structural and functional insights in flavivirus NS5 proteins gained by the structure of Ntaya virus polymerase and methyltransferase. Structure 2024; 32:1099-1109.e3. [PMID: 38781970 DOI: 10.1016/j.str.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Flaviviruses are single-stranded positive-sense RNA (+RNA) viruses that are responsible for several (re)emerging diseases such as yellow, dengue, or West Nile fevers. The Zika epidemic highlighted their dangerousness when a relatively benign virus known since the 1950s turned into a deadly pathogen. The central protein for their replication is NS5 (non-structural protein 5), which is composed of the N-terminal methyltransferase (MTase) domain and the C-terminal RNA-dependent RNA-polymerase (RdRp) domain. It is responsible for both RNA replication and installation of the 5' RNA cap. We structurally and biochemically analyzed the Ntaya virus MTase and RdRp domains and we compared their properties to other flaviviral NS5s. The enzymatic centers are well conserved across Flaviviridae, suggesting that the development of drugs targeting all flaviviruses is feasible. However, the enzymatic activities of the isolated proteins were significantly different for the MTase domains.
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Affiliation(s)
- Kateřina Krejčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic; Faculty of Sciences, Charles University, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Karel Chalupsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Eva Zilecka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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6
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Goh JZH, De Hayr L, Khromykh AA, Slonchak A. The Flavivirus Non-Structural Protein 5 (NS5): Structure, Functions, and Targeting for Development of Vaccines and Therapeutics. Vaccines (Basel) 2024; 12:865. [PMID: 39203991 PMCID: PMC11360482 DOI: 10.3390/vaccines12080865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/20/2024] [Accepted: 07/27/2024] [Indexed: 09/03/2024] Open
Abstract
Flaviviruses, including dengue (DENV), Zika (ZIKV), West Nile (WNV), Japanese encephalitis (JEV), yellow fever (YFV), and tick-borne encephalitis (TBEV) viruses, pose a significant global emerging threat. With their potential to cause widespread outbreaks and severe health complications, the development of effective vaccines and antiviral therapeutics is imperative. The flaviviral non-structural protein 5 (NS5) is a highly conserved and multifunctional protein that is crucial for viral replication, and the NS5 protein of many flaviviruses has been shown to be a potent inhibitor of interferon (IFN) signalling. In this review, we discuss the functions of NS5, diverse NS5-mediated strategies adopted by flaviviruses to evade the host antiviral response, and how NS5 can be a target for the development of vaccines and antiviral therapeutics.
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Affiliation(s)
| | | | | | - Andrii Slonchak
- Australian Infectious Diseases Research Center, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (J.Z.H.G.); (L.D.H.); (A.A.K.)
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7
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Panday H, Jha SK, Al-Shehri M, Panda SP, Rana R, Alwathinani NF, Azhar EI, Dwivedi VD, Jha AK. Allosteric inhibition of dengue virus RNA-dependent RNA polymerase by Litsea cubeba phytochemicals: a computational study. J Biomol Struct Dyn 2024; 42:5402-5414. [PMID: 38764132 DOI: 10.1080/07391102.2023.2226759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/11/2023] [Indexed: 05/21/2024]
Abstract
RNA-dependent RNA polymerase (RdRp) is considered a potential drug target for dengue virus (DENV) inhibition and has attracted attention in antiviral drug discovery. Here, we screened 121 natural compounds from Litsea cubeba against DENV RdRp using various approaches of computer-based drug discovery. Notably, we identified four potential compounds (Ushinsunine, Cassameridine, (+)-Epiexcelsin, (-)-Phanostenine) with good binding scores and allosteric interactions with the target protein. Moreover, molecular dynamics simulation studies were done to check the conformational stability of the complexes under given conditions. Additionally, we performed post-simulation analysis to find the stability of potential drugs in the target protein. The findings suggest Litsea cubeba-derived phytomolecules as a therapeutic solution to control DENV infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hrithika Panday
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Mohammed Al-Shehri
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Nada F Alwathinani
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biology, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Abhimanyu Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
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8
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Cheng C, Tan MJA, Chan KWK, Choy MMJ, Roman N, Arnold DDR, Bifani AM, Kong SYZ, Bist P, Nath BK, Swarbrick CMD, Forwood JK, Vasudevan SG. Serotype-Specific Regulation of Dengue Virus NS5 Protein Subcellular Localization. ACS Infect Dis 2024; 10:2047-2062. [PMID: 38811007 PMCID: PMC11184549 DOI: 10.1021/acsinfecdis.4c00054] [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: 01/17/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024]
Abstract
Dengue virus (DENV) nonstructural protein 5 (NS5), consisting of methyltransferase and RNA-dependent RNA polymerase (RdRp) domains, is critical for viral RNA synthesis within endoplasmic reticulum-derived replication complexes in the cytoplasm. However, a significant proportion of NS5 is localized to the nucleus of infected cells for DENV2, 3, and 4, whereas DENV1 NS5 is localized diffusely in the cytoplasm. We still have an incomplete understanding of how the DENV NS5 subcellular localization is regulated. Within NS5, two putative nuclear localization signal (NLS) sequences have been identified: NLSCentral residing in the palm of the RdRp domain as well as the recently discovered NLSC-term residing in the flexible region at the C-terminal of the RdRp domain. We have previously shown that DENV2 NS5 nuclear localization can be significantly reduced by single-point mutations to the NLSC-term. Here, we present biochemical, virological, and structural data demonstrating that the relative importance of either NLS in NS5 nuclear localization is unique to each of the four DENV serotypes. DENV1 NS5's cytoplasmic localization appears to be due to a functionally weak interaction between its NLSCentral and importin-α (IMPα), while DENV2 NS5 is almost exclusively nuclear through its NLSC-term's strong interaction with IMPα. Both NLSs of DENV3 NS5 appear to contribute to directing its nuclear localization. Lastly, in the case of DENV4, the regulation of its NS5 nuclear localization remains an enigma but appears to be associated with its NLSC-term.
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Affiliation(s)
- Colin
Xinru Cheng
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Min Jie Alvin Tan
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Kitti Wing Ki Chan
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Milly Ming Ju Choy
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Noelia Roman
- School
of Dentistry and Medical Sciences, Charles
Sturt University, Wagga
Wagga, NSW 2678, Australia
| | - Daniel D. R. Arnold
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
- School
of Dentistry and Medical Sciences, Charles
Sturt University, Wagga
Wagga, NSW 2678, Australia
| | - Amanda Makha Bifani
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Sean Yao Zu Kong
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Pradeep Bist
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
| | - Babu K. Nath
- School
of Dentistry and Medical Sciences, Charles
Sturt University, Wagga
Wagga, NSW 2678, Australia
| | - Crystall M. D. Swarbrick
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
- Biosecurity
Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Institute
for Glycomics, Griffith University, Southport 4222, Australia
| | - Jade K. Forwood
- School
of Dentistry and Medical Sciences, Charles
Sturt University, Wagga
Wagga, NSW 2678, Australia
- Biosecurity
Research Program and Training Centre, Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Subhash G. Vasudevan
- Programme
in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore 169857, Singapore
- Department
of Microbiology and Immunology, National
University of Singapore, Singapore 117545, Singapore
- Institute
for Glycomics, Griffith University, Southport 4222, Australia
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9
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Wang X, Jing X, Shi J, Liu Q, Shen S, Cheung PPH, Wu J, Deng F, Gong P. A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase. Nucleic Acids Res 2024; 52:3278-3290. [PMID: 38296832 PMCID: PMC11014250 DOI: 10.1093/nar/gkae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Jingmenviruses are a category of emerging segmented viruses that have garnered global attention in recent years, and are close relatives of the flaviviruses in the Flaviviridae family. One of their genome segments encodes NSP1 homologous to flavivirus NS5. NSP1 comprises both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRP) modules playing essential roles in viral genome replication and capping. Here we solved a 1.8-Å resolution crystal structure of the NSP1 RdRP module from Jingmen tick virus (JMTV), the type species of jingmenviruses. The structure highly resembles flavivirus NS5 RdRP despite a sequence identity less than 30%. NSP1 RdRP enzymatic properties were dissected in a comparative setting with several representative Flaviviridae RdRPs included. Our data indicate that JMTV NSP1 produces characteristic 3-mer abortive products similar to the hepatitis C virus RdRP, and exhibits the highest preference of terminal initiation and shorter-primer usage. Unlike flavivirus NS5, JMTV RdRP may require the MTase for optimal transition from initiation to elongation, as an MTase-less NSP1 construct produced more 4-5-mer intermediate products than the full-length protein. Taken together, this work consolidates the evolutionary relationship between the jingmenvirus group and the Flaviviridae family, providing a basis to the further understanding of their viral replication/transcription process.
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Affiliation(s)
- Xinyu Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuping Jing
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Junming Shi
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Qiaojie Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Shu Shen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China
| | - Jiqin Wu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin 300350, China
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10
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Huq AKMM, Roney M, Dubey A, Nasir MH, Tufail A, Aluwi MFFM, Ishak WMW, Islam MR, Tajuddin SN. Phenolic compounds of Theobroma cacao L. show potential against dengue RdRp protease enzyme inhibition by In-silico docking, DFT study, MD simulation and MMGBSA calculation. PLoS One 2024; 19:e0299238. [PMID: 38483871 PMCID: PMC10939188 DOI: 10.1371/journal.pone.0299238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/03/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Currently, there is no antiviral medication for dengue, a potentially fatal tropical infectious illness spread by two mosquito species, Aedes aegypti and Aedes albopictus. The RdRp protease of dengue virus is a potential therapeutic target. This study focused on the in silico drug discovery of RdRp protease inhibitors. METHODS To assess the potential inhibitory activity of 29 phenolic acids from Theobroma cacao L. against DENV3-NS5 RdRp, a range of computational methods were employed. These included docking, drug-likeness analysis, ADMET prediction, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. The aim of these studies was to confirm the stability of the ligand-protein complex and the binding pose identified during the docking experiment. RESULTS Twenty-one compounds were found to have possible inhibitory activities against DENV according to the docking data, and they had a binding affinity of ≥-37.417 kcal/mol for DENV3- enzyme as compared to the reference compound panduratin A. Additionally, the drug-likeness investigation produced four hit compounds that were subjected to ADMET screening to obtain the lead compound, catechin. Based on ELUMO, EHOMO, and band energy gap, the DFT calculations showed strong electronegetivity, favouravle global softness and chemical reactivity with considerable intra-molecular charge transfer between electron-donor to electron-acceptor groups for catechin. The MD simulation result also demonstrated favourable RMSD, RMSF, SASA and H-bonds in at the binding pocket of DENV3-NS5 RdRp for catechin as compared to panduratin A. CONCLUSION According to the present findings, catechin showed high binding affinity and sufficient drug-like properties with the appropriate ADMET profiles. Moreover, DFT and MD studies further supported the drug-like action of catechin as a potential therapeutic candidate. Therefore, further in vitro and in vivo research on cocoa and its phytochemical catechin should be taken into consideration to develop as a potential DENV inhibitor.
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Affiliation(s)
- A. K. M. Moyeenul Huq
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Department of Pharmacy, School of Medicine, University of Asia Pacific, Dhaka, Bangladesh
| | - Miah Roney
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Muhammad Hassan Nasir
- Faculty of Medicine, University Sultan Zainal Abidin (UniSZA), Kuala Terengganu, Terengganu Darul Iman, Malaysia
| | - Aisha Tufail
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
| | - Wan Maznah Wan Ishak
- Faculty of Chemical and Processing Engineering Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
| | | | - Saiful Nizam Tajuddin
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, Kuantan, Pahang Darul Makmur, Malaysia
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11
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Biswal M, Yao W, Lu J, Chen J, Morrison J, Hai R, Song J. A conformational selection mechanism of flavivirus NS5 for species-specific STAT2 inhibition. Commun Biol 2024; 7:76. [PMID: 38195857 PMCID: PMC10776582 DOI: 10.1038/s42003-024-05768-8] [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: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
Flaviviruses, including Zika virus (ZIKV) and Dengue virus (DENV), rely on their non-structural protein 5 (NS5) for both replication of viral genome and suppression of host IFN signaling. DENV and ZIKV NS5s were shown to facilitate proteosome-mediated protein degradation of human STAT2 (hSTAT2). However, how flavivirus NS5s have evolved for species-specific IFN-suppression remains unclear. Here we report structure-function characterization of the DENV serotype 2 (DENV2) NS5-hSTAT2 complex. The MTase and RdRP domains of DENV2 NS5 form an extended conformation to interact with the coiled-coil and N-terminal domains of hSTAT2, thereby promoting hSTAT2 degradation in cells. Disruption of the extended conformation of DENV2/ZIKV NS5, but not the alternative compact state, impaired their hSTAT2 binding. Our comparative structural analysis of flavivirus NS5s further reveals a conserved protein-interaction platform with subtle amino-acid variations likely underpinning diverse IFN-suppression mechanisms. Together, this study uncovers a conformational selection mechanism underlying species-specific hSTAT2 inhibition by flavivirus NS5.
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Affiliation(s)
- Mahamaya Biswal
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Wangyuan Yao
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Jianbin Chen
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Rong Hai
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, USA.
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12
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Koraboina CP, Akshinthala P, Katari NK, Adarasandi R, Jonnalagadda SB, Gundla R. New oxindole carboxamides as inhibitors of DENV NS5 RdRp: Design, synthesis, docking and Biochemical characterization. Heliyon 2023; 9:e21510. [PMID: 38027588 PMCID: PMC10665688 DOI: 10.1016/j.heliyon.2023.e21510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Dengue is a mosquito-borne disease caused by the dengue virus belonging to family flaviviridae and has grown to be a major global public health issue. Despite decades of effort, the global comeback of dengue is evidence of the inadequacy of present management techniques. Due to the loss of healthy lives and the depletion of scarce medical resources, dengue has a significant negative economic impact in underdeveloped countries. In recent years, research for tackling the incidences of dengue infection has increased. The structure of the viral genome has been deciphered with the non-structural protein, known as NS5 serving as a potential target. NS5 consisting of an MTase domain involved in RNA capping and an RdRp domain involved in viral replication. In the presented work, a series of new Oxindoline Carboxamide derivatives were designed and synthesized for inhibiting the viral RNA dependent RNA-polymerase (RdRp) activity of DENV. The novel compounds were put through tests including molecular docking and surface plasmon resonance (SPR) binding analysis to evaluate their affinity for the viral protein and their potential as novel inhibitors of the virus. From a total of 12 derivative compounds, four compounds OCA-10c, OCA-10f, OCA-10j & OCA-10i, were found to exhibit high affinity for NS5 RdRp, the KD values being 1.376 μM, 1.63 μM, 7.08 μM & 9.32 μM respectively. Overall, we report novel inhibitors of DENV RdRp activity with potential to be utilized against DENV for treating humans after further optimization.
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Affiliation(s)
- Chandra Prakash Koraboina
- Department of Chemistry, School of Science, GITAM (Deemed to be University) Hyderabad, Telangana, 502 329, India
| | - Parameswari Akshinthala
- Department of Science and Humanities, MLR Institute of Technology, Dundigal, Medchal, Hyderabad, Telangana, 500 043, India
| | - Naresh Kumar Katari
- Department of Chemistry, School of Science, GITAM (Deemed to be University) Hyderabad, Telangana, 502 329, India
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, Westville Campus, University of KwaZulu-Natal, P Bag X 54001, Durban, 4000, South Africa
| | - Ravi Adarasandi
- Department of Chemistry, School of Science, GITAM (Deemed to be University) Hyderabad, Telangana, 502 329, India
| | - Sreekantha Babu Jonnalagadda
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, Westville Campus, University of KwaZulu-Natal, P Bag X 54001, Durban, 4000, South Africa
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM (Deemed to be University) Hyderabad, Telangana, 502 329, India
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13
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Mensah IK, Norvil AB, He M, Lendy E, Hjortland N, Tan H, Pomerantz RT, Mesecar A, Gowher H. Development of a sensitive microplate assay for characterizing RNA methyltransferase activity: Implications for epitranscriptomics and drug development. J Biol Chem 2023; 299:105257. [PMID: 37716702 PMCID: PMC10582764 DOI: 10.1016/j.jbc.2023.105257] [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: 01/25/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023] Open
Abstract
RNA methylation is a ubiquitous post-transcriptional modification found in diverse RNA classes and is a critical regulator of gene expression. In this study, we used Zika virus RNA methyltransferase (MTase) to develop a highly sensitive microplate assay that uses a biotinylated RNA substrate and radiolabeled AdoMet coenzyme. The assay is fast, highly reproducible, exhibits linear progress-curve kinetics under multiple turnover conditions, has high sensitivity in competitive inhibition assays, and significantly lower background levels compared with the currently used method. Using our newly developed microplate assay, we observed no significant difference in the catalytic constants of the full-length nonstructural protein 5 enzyme and the truncated MTase domain. These data suggest that, unlike the Zika virus RNA-dependent RNA polymerase activity, the MTase activity is unaffected by RNA-dependent RNA polymerase-MTase interdomain interaction. Given its quantitative nature and accuracy, this method can be used to characterize various RNA MTases, and, therefore, significantly contribute to the field of epitranscriptomics and drug development against infectious diseases.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Allison B Norvil
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Ming He
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Emma Lendy
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Nicole Hjortland
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Hern Tan
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Richard T Pomerantz
- Department Biochemistry and Molecular Biology, Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania, USA
| | - Andrew Mesecar
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA.
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14
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Fang X, Lu G, Deng Y, Yang S, Hou C, Gong P. Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding. Virol Sin 2023; 38:531-540. [PMID: 37156298 PMCID: PMC10436059 DOI: 10.1016/j.virs.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
The Dicistroviridae is a virus family that includes many insect pathogens. These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase (RdRP) also named 3Dpol. Compared with the Picornaviridae RdRPs such as poliovirus (PV) 3Dpol, the Dicistroviridae representative Israeli acute paralysis virus (IAPV) 3Dpol has an additional N-terminal extension (NE) region that is about 40-residue in length. To date, both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive. Here we reported crystal structures of two truncated forms of IAPV 3Dpol, namely Δ85 and Δ40, both missing the NE region, and the 3Dpol protein in these structures exhibited three conformational states. The palm and thumb domains of these IAPV 3Dpol structures are largely consistent with those of the PV 3Dpol structures. However, in all structures, the RdRP fingers domain is partially disordered, while different conformations of RdRP substructures and interactions between them are also present. In particular, a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of the Δ40 structure, while a previously documented alternative conformation of motif A was observed in all IAPV structures. These experimental data on one hand show intrinsic conformational variances of RdRP substructures, and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.
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Affiliation(s)
- Xiang Fang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China
| | - Yanchun Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chunsheng Hou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430207, China.
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15
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Bhatnagar P, Bajpai P, Shrinet J, Kaja MK, Chandele A, Sitaraman R. Prediction of human protein interactome of dengue virus non-structural protein 5 (NS5) and its downstream immunological implications. 3 Biotech 2023; 13:180. [PMID: 37193327 PMCID: PMC10182223 DOI: 10.1007/s13205-023-03569-0] [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: 10/06/2022] [Accepted: 04/19/2023] [Indexed: 05/18/2023] Open
Abstract
The non-structural protein 5 (NS5) is the most conserved protein among flaviviruses, a family that includes the dengue virus. It functions both as an RNA-dependent RNA polymerase and an RNA-methyltransferase and is therefore essential for the replication of viral RNA. The discovery that dengue virus NS5 protein (DENV-NS5) can also localize to the nucleus has resulted in renewed interest in its potential roles at the host-virus interface. In this study, we have used two complementary computational approaches in parallel - one based on linear motifs (ELM) and another based on tertiary structure of the protein (DALI) - to predict the host proteins that DENV-NS5 might interact with. Of the 42 human proteins predicted by both these methods, 34 are novel. Pathway analysis of these 42 human proteins shows that they are involved in key host cellular processes related to cell cycle regulation, proliferation, protein degradation, apoptosis, and immune responses. A focused analysis of transcription factors that directly interact with the predicted DENV-NS5 interacting proteins was performed, followed by the identification of downstream genes that are differentially expressed after dengue infection using previously published RNA-seq data. Our study provides unique insights into the DENV-NS5 interaction network and delineates mechanisms whereby DENV-NS5 could impact the host-virus interface. The novel interactors identified in this study could be potentially targeted by NS5 to modulate the host cellular environment in general, and the immune response in particular, thereby extending the role of DENV-NS5 beyond its known enzymatic functions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03569-0.
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Affiliation(s)
- Priya Bhatnagar
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi, India
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Jatin Shrinet
- Department of Biological Science, Florida State University, Tallahassee, FL 32306 USA
| | - Murali Krishna Kaja
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Department of Pediatrics and Emory Vaccine Centre, Emory University School of Medicine, Atlanta, GA USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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16
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Sreekanth GP. Perspectives on the current antiviral developments towards RNA-dependent RNA polymerase (RdRp) and methyltransferase (MTase) domains of dengue virus non-structural protein 5 (DENV-NS5). Eur J Med Chem 2023; 256:115416. [PMID: 37159959 DOI: 10.1016/j.ejmech.2023.115416] [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: 02/13/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Dengue virus (DENV) infection is one of the most emerging arboviral infections in humans. DENV is a positive-stranded RNA virus in the Flaviviridae family consisting of an 11 kb genome. DENV non-structural protein 5 (DENV-NS5) constitutes the largest among the non-structural proteins, which act as two domains, the RNA-dependent RNA polymerase (RdRp) and RNA methyltransferase enzyme (MTase). The DENV-NS5 RdRp domain contributes to the viral replication stages, whereas the MTase initiates viral RNA capping and facilitates polyprotein translation. Given the functions of both DENV-NS5 domains have made them an important druggable target. Possible therapeutic interventions and drug discoveries against DENV infection were thoroughly reviewed; however, a current update on the therapeutic strategies specific to DENV-NS5 or its active domains was not attempted. Since most potential compounds and drugs targeting the DENV-NS5 were evaluated in both in vitro cultures and animal models, a more detailed evaluation of molecules/drug candidates still requires investigation in randomized controlled clinical trials. This review summarizes current perspectives on the therapeutic strategies adopted to target the DENV-NS5 (RdRp and MTase domains) at the host-pathogen interface and further discusses the directions to identify candidate drugs to combat DENV infection.
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Affiliation(s)
- Gopinathan Pillai Sreekanth
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad-500007, Telangana, India.
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17
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Zhu Y, Liang M, Yu J, Zhang B, Zhu G, Huang Y, He Z, Yuan J. Repurposing of Doramectin as a New Anti-Zika Virus Agent. Viruses 2023; 15:v15051068. [PMID: 37243154 DOI: 10.3390/v15051068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Zika virus (ZIKV), belonging to the Flavivirus family and mainly transmitted by mosquitoes, causes a variety of adverse outcomes, including Guillain-Barré syndrome, microcephaly, and meningoencephalitis. However, there are no approved vaccines or drugs available for ZIKV. The discovery and research on drugs for ZIKV are still essential. In this study, we identified doramectin, an approved veterinary antiparasitic drug, as a novel anti-ZIKV agent (EC50 value from 0.85 μM to 3.00 μM) with low cytotoxicity (CC50 > 50 μM) in multiple cellular models. The expression of ZIKV proteins also decreased significantly under the treatment of doramectin. Further study showed that doramectin directly interacted with the key enzyme for ZIKV genome replication, RNA-dependent RNA polymerase (RdRp), with a stronger affinity (Kd = 16.9 μM), which may be related to the effect on ZIKV replication. These results suggested that doramectin might serve as a promising drug candidate for anti-ZIKV.
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Affiliation(s)
- Yujia Zhu
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Minqi Liang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Jianchen Yu
- School of Chemistry, South China Normal University, Guangzhou 510006, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Bingzhi Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Ge Zhu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yun Huang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhenjian He
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Jie Yuan
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
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18
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Nonyong P, Ekalaksananan T, Phanthanawiboon S, Overgaard HJ, Alexander N, Thaewnongiew K, Sawaswong V, Nimsamer P, Payungporn S, Phadungsombat J, Nakayama EE, Shioda T, Pientong C. Intrahost Genetic Diversity of Dengue Virus in Human Hosts and Mosquito Vectors under Natural Conditions Which Impact Replicative Fitness In Vitro. Viruses 2023; 15:982. [PMID: 37112962 PMCID: PMC10143933 DOI: 10.3390/v15040982] [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: 02/04/2023] [Revised: 04/08/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Dengue virus (DENV) is an arbovirus whose transmission cycle involves disparate hosts: humans and mosquitoes. The error-prone nature of viral RNA replication drives the high mutation rates, and the consequently high genetic diversity affects viral fitness over this transmission cycle. A few studies have been performed to investigate the intrahost genetic diversity between hosts, although their mosquito infections were performed artificially in the laboratory setting. Here, we performed whole-genome deep sequencing of DENV-1 (n = 11) and DENV-4 (n = 13) derived from clinical samples and field-caught mosquitoes from the houses of naturally infected patients, in order to analyze the intrahost genetic diversity of DENV between host types. Prominent differences in DENV intrahost diversity were observed in the viral population structure between DENV-1 and DENV-4, which appear to be associated with differing selection pressures. Interestingly, three single amino acid substitutions in the NS2A (K81R), NS3 (K107R), and NS5 (I563V) proteins in DENV-4 appear to be specifically acquired during infection in Ae. aegypti mosquitoes. Our in vitro study shows that the NS2A (K81R) mutant replicates similarly to the wild-type infectious clone-derived virus, while the NS3 (K107R), and NS5 (I563V) mutants have prolonged replication kinetics in the early phase in both Vero and C6/36 cells. These findings suggest that DENV is subjected to selection pressure in both mosquito and human hosts. The NS3 and NS5 genes may be specific targets of diversifying selection that play essential roles in early processing, RNA replication, and infectious particle production, and they are potentially adaptive at the population level during host switching.
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Affiliation(s)
- Patcharaporn Nonyong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Supranee Phanthanawiboon
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
| | - Hans J. Overgaard
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway;
| | - Neal Alexander
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Kesorn Thaewnongiew
- Department of Disease Control, Office of Disease Prevention and Control, Region 7 Khon Kaen, Ministry of Public Health, Khon Kaen 40000, Thailand;
| | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
| | - Pattaraporn Nimsamer
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
| | - Sunchai Payungporn
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (P.N.); (S.P.)
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
| | - Emi E. Nakayama
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (P.N.); (T.E.); (S.P.)
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen 40002, Thailand
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19
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Felicetti T, Gwee CP, Burali MS, Chan KWK, Alonso S, Pismataro MC, Sabatini S, Barreca ML, Cecchetti V, Vasudevan SG, Manfroni G. Functionalized sulfonyl anthranilic acid derivatives inhibit replication of all the four dengue serotypes. Eur J Med Chem 2023; 252:115283. [PMID: 36965228 DOI: 10.1016/j.ejmech.2023.115283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Dengue virus (DENV), a mosquito-borne flavivirus, continues to be a major public health threat in many countries and no approved antiviral therapeutics are available yet. In this work, we designed and synthesized a series of sulfonyl anthranilic acid (SAA) derivatives using a ligand-based scaffold morphing approach of the 2,1-benzothiazine 2,2-dioxide core, previously used by us to develop DENV polymerase inhibitors resulting devoid of any cell-based antiviral activity. Several derivatives based on the new SAA chemotype exhibited potent inhibition against DENV infection in the cell-based assay but did not inhibit DENV NS5 polymerase activity in the in vitro de novo initiation and elongation assays. Notably, best compounds 26 and 39 showed EC50 values in the range of 0.54-1.36 μM against cells infected with the four dengue serotypes (DENV-1-4). Time-of-drug-addition assay revealed that analogue 26 is a post-entry replication inhibitor that appears to be specific for cells of primate origin, implicating a host target with a high barrier to resistance. In conclusion, SAA derivatives offer a valuable starting point for developing effective Dengue antiviral therapeutics.
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Affiliation(s)
- Tommaso Felicetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Chin Piaw Gwee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Maria Sole Burali
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Sylvie Alonso
- Infectious Diseases Translational Research Programme, Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, Singapore; Immunology programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Maria Chiara Pismataro
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Stefano Sabatini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Maria Letizia Barreca
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Violetta Cecchetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Institute for Glycomics, Griffith University, Queensland, 4222, Australia.
| | - Giuseppe Manfroni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy.
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20
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van den Elsen K, Chew BLA, Ho JS, Luo D. Flavivirus nonstructural proteins and replication complexes as antiviral drug targets. Curr Opin Virol 2023; 59:101305. [PMID: 36870091 PMCID: PMC10023477 DOI: 10.1016/j.coviro.2023.101305] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/02/2023] [Accepted: 01/17/2023] [Indexed: 03/06/2023]
Abstract
Many flaviviruses are well-known pathogens, such as dengue, Zika, Japanese encephalitis, and yellow fever viruses. Among them, dengue viruses cause global epidemics and threaten billions of people. Effective vaccines and antivirals are in desperate need. In this review, we focus on the recent advances in understanding viral nonstructural (NS) proteins as antiviral drug targets. We briefly summarize the experimental structures and predicted models of flaviviral NS proteins and their functions. We highlight a few well-characterized inhibitors targeting these NS proteins and provide an update about the latest development. NS4B emerges as one of the most promising drug targets as novel inhibitors targeting NS4B and its interaction network are entering clinical studies. Studies aiming to elucidate the architecture and molecular basis of viral replication will offer new opportunities for novel antiviral discovery. Direct-acting agents against dengue and other pathogenic flaviviruses may be available very soon.
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Affiliation(s)
- Kaïn van den Elsen
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Bing Liang Alvin Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Jun Sheng Ho
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore.
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21
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Roy KK, Jyothi D, Paul U, Sukla S. Identification and validation of novel non-nucleoside class of molecules inhibiting the dengue virus replication. J Biomol Struct Dyn 2023; 41:13993-14002. [PMID: 36970872 DOI: 10.1080/07391102.2023.2192796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/29/2023] [Indexed: 03/29/2023]
Abstract
There is currently no drug available to treat mosquito-borne dengue. The C-terminal RNA-dependent RNA polymerase (RdRp) domain in the non-structural type 5 (NS5) protein of the dengue virus (DENV) is essential for viral RNA synthesis and replication, and therefore, it is an attractive target for the anti-dengue drug development. We report herein the discovery and validation of two novel non-nucleoside classes of small molecules as DENV RdRp inhibitors. Firstly, using the refined X-ray structure of the DENV NS5 RdRp domain (PDB-ID: 4V0R), we conducted docking, binding free-energy studies, and short-scale molecular dynamics simulation to investigate the binding sites of known small molecules that led to the optimized protein-ligand complex. Subsequently, protein structure-based screening of a commercial database (∼500,000 synthetic compounds), pre-filtered for the drug-likeness, led to the top-ranked 171 molecules, which was then subjected to structural diversity analysis and clustering. This process led to six structurally distinct and best-scored compounds that were procured from the commercial vendor, and then subjected to the in vitro testing in the MTT and dengue infection assays. It revealed two unique and structurally unique compounds, KKR-D-02 and KKR-D-03, exhibiting 84 and 81% reductions, respectively, in DENV copy number in repeated assays in comparison to the virus-infected cell controls. These active compounds represent novel scaffolds for further structure-based discovery of novel candidate molecules for the intervention of dengue.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kuldeep K Roy
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES University, Dehradun, Uttarakhand, India
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Deeti Jyothi
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Udita Paul
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Soumi Sukla
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Chunilal Bhawan, Kolkata, West Bengal, India
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22
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Lee MF, Wu YS, Poh CL. Molecular Mechanisms of Antiviral Agents against Dengue Virus. Viruses 2023; 15:v15030705. [PMID: 36992414 PMCID: PMC10056858 DOI: 10.3390/v15030705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Dengue is a major global health threat causing 390 million dengue infections and 25,000 deaths annually. The lack of efficacy of the licensed Dengvaxia vaccine and the absence of a clinically approved antiviral against dengue virus (DENV) drive the urgent demand for the development of novel anti-DENV therapeutics. Various antiviral agents have been developed and investigated for their anti-DENV activities. This review discusses the mechanisms of action employed by various antiviral agents against DENV. The development of host-directed antivirals targeting host receptors and direct-acting antivirals targeting DENV structural and non-structural proteins are reviewed. In addition, the development of antivirals that target different stages during post-infection such as viral replication, viral maturation, and viral assembly are reviewed. Antiviral agents designed based on these molecular mechanisms of action could lead to the discovery and development of novel anti-DENV therapeutics for the treatment of dengue infections. Evaluations of combinations of antiviral drugs with different mechanisms of action could also lead to the development of synergistic drug combinations for the treatment of dengue at any stage of the infection.
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23
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Identification of West Nile virus RNA-dependent RNA polymerase non-nucleoside inhibitors by real-time high throughput fluorescence screening. Antiviral Res 2023; 212:105568. [PMID: 36842536 DOI: 10.1016/j.antiviral.2023.105568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023]
Abstract
West Nile virus (WNV) is a re-emergent mosquito-borne RNA virus that causes major outbreaks of encephalitis around the world. However, there is no therapeutic treatment to struggle against WNV, and the current treatment relies on alleviating symptoms. Therefore, due to the threat virus poses to animal and human health, there is an urgent need to come up with fast strategies to identify and assess effective antiviral compounds. A relevant target when developing drugs against RNA viruses is the viral RNA-dependent RNA polymerase (RdRp), responsible for the replication of the viral genome within a host cell. RdRps are key therapeutic targets based on their specificity for RNA and their essential role in the propagation of the infection. We have developed a fluorescence-based method to measure WNV RdRp activity in a fast and reliable real-time way. Interestingly, rilpivirine has shown in our assay inhibition of the WNV RdRp activity with an IC50 value of 3.3 μM and its antiviral activity was confirmed in cell cultures. Furthermore, this method has been extended to build up a high-throughput screening platform to identify WNV polymerase inhibitors. By screening a small chemical library, novel RdRp inhibitors 1-4 have been identified. When their antiviral activity was tested against WNV in cell culture, 4 exhibited an EC50 value of 2.5 μM and a selective index of 12.3. Thus, rilpivirine shows up as an interesting candidate for repurposing against flavivirus. Moreover, the here reported method allows the rapid identification of new WNV RdRp inhibitors.
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24
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Norshidah H, Leow CH, Ezleen KE, Wahab HA, Vignesh R, Rasul A, Lai NS. Assessing the potential of NS2B/NS3 protease inhibitors biomarker in curbing dengue virus infections: In silico vs. In vitro approach. Front Cell Infect Microbiol 2023; 13:1061937. [PMID: 36864886 PMCID: PMC9971573 DOI: 10.3389/fcimb.2023.1061937] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023] Open
Abstract
An increase in the occurrence of viral infectious diseases is a global concern for human health. According to a WHO report, dengue virus (DENV) is one of the most common viral diseases affecting approximately 400 million people annually, with worsening symptoms in nearly 1% of cases. Both academic and industrial researchers have conducted numerous studies on viral epidemiology, virus structure and function, source and route of infection, treatment targets, vaccines, and drugs. The development of CYD-TDV or Dengvaxia® vaccine has been a major milestone in dengue treatment. However, evidence has shown that vaccines have some drawbacks and limitations. Therefore, researchers are developing dengue antivirals to curb infections. DENV NS2B/NS3 protease is a DENV enzyme essential for replication and virus assembly, making it an interesting antiviral target. For faster hit and lead recognition of DENV targets, methods to screen large number of molecules at lower costs are essential. Similarly, an integrated and multidisciplinary approach involving in silico screening and confirmation of biological activity is required. In this review, we discuss recent strategies for searching for novel DENV NS2B/NS3 protease inhibitors from the in silico and in vitro perspectives, either by applying one of the approaches or by integrating both. Therefore, we hope that our review will encourage researchers to integrate the best strategies and encourage further developments in this area.
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Affiliation(s)
- Harun Norshidah
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia,Universiti Kuala Lumpur-Royal College of Medicine Perak, Ipoh, Perak, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Ramachandran Vignesh
- Universiti Kuala Lumpur-Royal College of Medicine Perak, Ipoh, Perak, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
| | - Azhar Rasul
- Department of Zoology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Ngit Shin Lai
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
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25
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Malik M, Vijayan P, Jagannath DK, Mishra RK, Lakshminarasimhan A. Sofosbuvir and its tri-phosphate metabolite inhibit the RNA-dependent RNA polymerase activity of non-structural protein 5 from the Kyasanur forest disease virus. Biochem Biophys Res Commun 2023; 641:50-56. [PMID: 36521285 DOI: 10.1016/j.bbrc.2022.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Kyasanur forest disease is a neglected zoonotic disease caused by a single-stranded RNA-based flavivirus, the incidence of which was first recorded in 1957 in the Southern part of India. Kyasanur forest disease virus is transmitted to monkeys and humans through the infected tick bite of Haemophysalis spinigera. Kyasanur forest disease is a febrile illness, which in severe cases, results in neurological complications leading to mortality. The current treatment regimens are symptomatic and supportive, and no targeted therapies are available for this disease. In this study, we evaluated the ability of FDA-approved drugs sofosbuvir (and its active metabolite) and Dasabuvir to inhibit the RNA-dependent RNA polymerase activity of NS5 protein from the Kyasanur forest disease virus. NS5 protein containing the N-terminal methyl transferase domain and C-terminal RNA-dependent RNA polymerase domain was expressed in Escherichia coli, and RNA-dependent RNA polymerase activity was demonstrated with the purified protein. The RNA-dependent RNA polymerase assay conditions were optimized, followed by the determination of apparent Km,ATP to validate the enzyme preparation. Half maximal-inhibitory concentrations against RNA-dependent RNA polymerase activity were determined for Sofosbuvir and its active metabolite. Dasabuvir did not show detectable inhibition with the tested conditions. This is the first demonstration of the inhibition of RNA-dependent RNA polymerase activity of NS5 protein from the Kyasanur forest disease virus with small molecule inhibitors. These initial findings can potentially facilitate the discovery and development of targeted therapies for treating Kyasanur forest disease.
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Affiliation(s)
- Mansi Malik
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
| | - Parvathy Vijayan
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
| | - Deepak K Jagannath
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
| | - Rakesh K Mishra
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
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26
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Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases. Proc Natl Acad Sci U S A 2023; 120:e2211425120. [PMID: 36577062 PMCID: PMC9910504 DOI: 10.1073/pnas.2211425120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
De novo viral RNA-dependent RNA polymerases (RdRPs) utilize their priming element (PE) to facilitate accurate initiation. Upon transition to elongation, the PE has to retreat from the active site to give room to the template-product RNA duplex. However, PE conformational change upon this transition and the role of PE at elongation both remain elusive. Here, we report crystal structures of RdRP elongation complex (EC) from dengue virus serotype 2 (DENV2), demonstrating a dramatic refolding of PE that allows establishment of interactions with the RNA duplex backbone approved to be essential for EC stability. Enzymology data from both DENV2 and hepatitis C virus (HCV) RdRPs suggest that critical transition of the refolding likely occurs after synthesis of a 4- to 5-nucleotide (nt) product together providing a key basis in understanding viral RdRP transition from initiation to elongation.
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27
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Bhardwaj A, Sharma R, Grover A. Immuno-informatics guided designing of a multi-epitope vaccine against Dengue and Zika. J Biomol Struct Dyn 2023; 41:1-15. [PMID: 34796791 DOI: 10.1080/07391102.2021.2002720] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Dengue and zika are amongst the most prevalent mosquito-borne diseases caused by closely related members Dengue virus (DENV) and Zika virus (ZIKV), respectively, of the Flaviviridae family. DENV and ZIKV have been reported to co-infect several people, resulting in fatalities across the world. A vaccine that can safeguard against both these pathogens concurrently, can offer several advantages. This study has employed immuno-informatics for devising a multi-epitope, multi-pathogenic vaccine against both these viruses. Since, the two viruses share a common vector source, whose salivary components are reported to aid viral pathogenesis; antigenic salivary proteins from Aedes aegypti were also incorporated into the design of the vaccine along with conserved structural and non-structural viral proteins. Conserved B- and T-cell epitopes were identified for all the selected antigenic proteins. These epitopes were merged and further supplemented with β-defensin as an adjuvant, to yield an immunogenic vaccine construct. In-silico 3D modeling and structural validation of the vaccine construct was conducted, followed by its molecular docking and molecular dynamics simulation studies with human TLR2. Immune simulation study was also performed, and it further provided support that the designed vaccine can mount an effective immune response and hence provide protection against both DENV and ZIKV. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aditi Bhardwaj
- School of Biosciences & Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ritika Sharma
- School of Biotechnology, Jawaharlal Nehru University (JNU), Delhi, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University (JNU), Delhi, India
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28
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de Paula Junior VF, van Tilburg MF, Morais PA, Júnior FFM, Lima EG, Oliveira VTDS, Guedes MIF, Caetano EWS, Freire VN. Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket. Int J Mol Sci 2022; 23:ijms231710088. [PMID: 36077486 PMCID: PMC9456192 DOI: 10.3390/ijms231710088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3.
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Affiliation(s)
- Valdir Ferreira de Paula Junior
- Biotechnology & Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, Brazil
- Correspondence: ; Tel.: +55-859-8541-8255
| | | | - Pablo Abreu Morais
- Federal Institute of Education, Science and Technology of Ceará, Campus Horizonte, Horizonte 62884-105, Brazil
| | - Francisco Franciné Maia Júnior
- Departamento de Ciências Naturais, Matemática e Estatística, Universidade Federal Rural do Semi-Árido, Mossoró 59625-900, Brazil
| | - Elza Gadelha Lima
- Laboratório Central de Saúde Pública do Ceará (LACEN), Fortaleza 60120-002, Brazil
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29
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Sun YT, Varani G. Structure of the dengue virus RNA promoter. RNA (NEW YORK, N.Y.) 2022; 28:1210-1223. [PMID: 35750488 PMCID: PMC9380747 DOI: 10.1261/rna.079197.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Dengue virus, a single-stranded positive sense RNA virus, is the most prevalent mosquito-borne pathogen in the world. Like all RNA viruses, it uses conserved structural elements within its genome to control essential replicative steps. A 70 nt stem-loop RNA structure (called SLA), found at the 5'-end of the genome of all flaviviruses, functions as the promoter for viral replication. This highly conserved structure interacts with the viral polymerase NS5 to initiate RNA synthesis. Here, we report the NMR structure of a monomeric SLA from dengue virus serotype 1, assembled to high-resolution from independently folded structural elements. The DENV1 SLA has an L-shaped structure, where the top and side helices are coaxially stacked, and the bottom helix is roughly perpendicular to them. Because the sequence is highly conserved among different flavivirus genomes, it is very likely that the three-dimensional fold and local structure of SLA are also conserved among flaviviruses and required for efficient replication. This work provides structural insight into the dengue promoter and provides the foundation for the discovery of new antiviral drugs that target this essential replicative step.
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Affiliation(s)
- Yi-Ting Sun
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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30
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Pharmacophore-Model-Based Drug Repurposing for the Identification of the Potential Inhibitors Targeting the Allosteric Site in Dengue Virus NS5 RNA-Dependent RNA Polymerase. Viruses 2022; 14:v14081827. [PMID: 36016449 PMCID: PMC9412353 DOI: 10.3390/v14081827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Dengue virus (DENV) is the causative agent of DENV infection. To tackle DENV infection, the development of therapeutic molecules as direct-acting antivirals (DAAs) has been demonstrated as a truly effective approach. Among various DENV drug targets, non-structural protein 5 (NS5)-a highly conserved protein among the family Flaviviridae-carries the RNA-dependent RNA polymerase (DENVRdRp) domain at the C-terminal, and its "N-pocket" allosteric site is widely considered for anti-DENV drug development. Therefore, in this study, we developed a pharmacophore model by utilising 41 known inhibitors of the DENVRdRp domain, and performed model screening against the FDA's approved drug database for drug repurposing against DENVRdRp. Herein, drugs complying with the pharmacophore hypothesis were further processed through standard-precision (SP) and extra-precision (XP) docking scores (DSs) and binding pose refinement based on MM/GBSA binding energy (BE) calculations. This resulted in the identification of four potential potent drugs: (i) desmopressin (DS: -10.52, BE: -69.77 kcal/mol), (ii) rutin (DS: -13.43, BE: -67.06 kcal/mol), (iii) lypressin (DS: -9.84, BE: -67.65 kcal/mol), and (iv) lanreotide (DS: -8.72, BE: -64.7 kcal/mol). The selected drugs exhibited relevant interactions with the allosteric N-pocket of DENVRdRp, including priming-loop and entry-point residues (i.e., R729, R737, K800, and E802). Furthermore, 100 ns explicit-solvent molecular dynamics simulations and end-point binding free energy assessments support the considerable stability and free energy of the selected drugs in the targeted allosteric pocket of DENVRdRp. Hence, these four drugs, repurposed as potent inhibitors of the allosteric site of DENVRdRp, are recommended for further validation using experimental assays.
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31
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Caldwell HS, Pata JD, Ciota AT. The Role of the Flavivirus Replicase in Viral Diversity and Adaptation. Viruses 2022; 14:1076. [PMID: 35632818 PMCID: PMC9143365 DOI: 10.3390/v14051076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses include several emerging and re-emerging arboviruses which cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses readily alternate and adapt to different hosts and environments. Here, we review a subset of the different aspects of flaviviral biology which impact host switching and viral fitness. These include the mechanism of replication and structural biology of the NS3 and NS5 proteins, which reproduce the viral genome; rates of mutation resulting from this replication and the role of mutational frequency in viral fitness; and the theory of quasispecies evolution and how it contributes to our understanding of genetic and phenotypic plasticity.
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Affiliation(s)
- Haley S. Caldwell
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
| | - Janice D. Pata
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Alexander T. Ciota
- The Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Slingerlands, NY 12159, USA;
- Department of Biomedical Sciences, State University of New York at Albany, School of Public Health, Rensselaer, NY 12144, USA;
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Zeng M, Zhang W, Jiang B, Lu T, Hu T, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Zhang L, Cheng A, Merits A, Chen S. Role of the homologous MTase-RdRp interface of flavivirus intramolecular NS5 on duck tembusu virus. Vet Microbiol 2022; 269:109433. [PMID: 35489297 DOI: 10.1016/j.vetmic.2022.109433] [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: 12/22/2021] [Revised: 03/08/2022] [Accepted: 04/10/2022] [Indexed: 11/26/2022]
Abstract
Flavivirus nonstructural protein 5 (NS5) harbors the N-terminal methyltransferase (MTase) and C-terminal polymerase RNA-dependent RNA polymerase (RdRp). The intramolecular NS5 features an integral MTase and RdRp interface with two components: a six-residue hydrophobic network and a GTR linker. Herein, the determinants of the MTase-RdRp interface and flavivirus substituted GTR linker were explored in TMUV replication and proliferation. First, the NanoLuc® Binary Technology (NanoBiT) and coimmunoprecipitation assays (Co-IP) methods confirmed the interaction between the MTase and RdRp domains of TMUV NS5. To screen for an optimal orientation for reporter gene fusion to the protein of interest, the signal activity of eight combinations of MTase and RdRp was explored. Intriguingly, all the combinations with the reporter gene fused to the C-terminal of MTase (1.1 C/2.1 C MTase) could barely detect any positive signal, suggesting a role for the GTR linker of the MTase C-terminal in MTase-RdRp affinity. Based on the flavivirus NS5 homologous interplay, we introduced alanine mutations into the MTase-RdRp interface of TMUV NS5. However, no single or pairwise mutation was found to abort the NS5 intramolecular interaction. Then, a mutated replicon and infectious clone were constructed to analyze the replication ability and properties of the recombinant virus. The mutant replicons of MTase F113A and M115A replicated to comparable extent as the wild type (WT). However, the replication level of the mutant MTase W121A was impaired without an obvious decrease in proliferation and virulence. Both the RdRp F351A and P585A mutants could replicate and proliferate well. Notably, the RdRp F467A virus was attenuated and did not strikingly impair the MTase-RdRp interaction. Furthermore, the TMUV was specifically compatible with the substituted NS5 with a Japanese encephalitis virus (JEV) GTR linker. Compensatory mutations were observed in the context of a defective MTase-RdRp interface after several passages of the rescued mutants in BHK-21 cells. A greater understanding of the molecular mechanism of the NS5 protein controlling duck TMUV replication will facilitate the design of novel therapies.
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Affiliation(s)
- Miao Zeng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Wei Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Bowen Jiang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Tong Lu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Tao Hu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Shaqiu Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Juan Huang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Xumin Ou
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Sai Mao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Qun Gao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Di Sun
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China
| | - Ling Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China.
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu 50090, Estonia
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, China.
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Exploring the structure, binding mode, flexibility and toxicity nature for Sinefungin molecule: a theoretical approach. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fishburn AT, Pham OH, Kenaston MW, Beesabathuni NS, Shah PS. Let's Get Physical: Flavivirus-Host Protein-Protein Interactions in Replication and Pathogenesis. Front Microbiol 2022; 13:847588. [PMID: 35308381 PMCID: PMC8928165 DOI: 10.3389/fmicb.2022.847588] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/31/2022] [Indexed: 12/23/2022] Open
Abstract
Flaviviruses comprise a genus of viruses that pose a significant burden on human health worldwide. Transmission by both mosquito and tick vectors, and broad host tropism contribute to the presence of flaviviruses globally. Like all viruses, they require utilization of host molecular machinery to facilitate their replication through physical interactions. Their RNA genomes are translated using host ribosomes, synthesizing viral proteins that cooperate with each other and host proteins to reshape the host cell into a factory for virus replication. Thus, dissecting the physical interactions between viral proteins and their host protein targets is essential in our comprehension of how flaviviruses replicate and how they alter host cell behavior. Beyond replication, even single interactions can contribute to immune evasion and pathogenesis, providing potential avenues for therapeutic intervention. Here, we review protein interactions between flavivirus and host proteins that contribute to virus replication, immune evasion, and disease.
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Affiliation(s)
- Adam T Fishburn
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Oanh H Pham
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Matthew W Kenaston
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Nitin S Beesabathuni
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States.,Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | - Priya S Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States.,Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
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Watanabe S, Chan KWK, Tan NWW, Mahid MBA, Chowdhury A, Chang KTE, Vasudevan SG. Experimental evidence for a high rate of maternal-fetal transmission of dengue virus in the presence of antibodies in immunocompromised mice. EBioMedicine 2022; 77:103930. [PMID: 35290828 PMCID: PMC8921544 DOI: 10.1016/j.ebiom.2022.103930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/15/2022] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Background Congenital disorders associated with prenatal vertical transmission of Zika virus (ZIKV) is well established since the 2016 outbreak in the Americas. However, despite clinical reports of similar mode of transmission for other flaviviruses such as dengue virus (DENV), the phenomenon has not been experimentally explored. Methods Pregnant AG129 mice were infected with DENV1 in the presence or absence of enhancing antibodies at different gestational time points. ZIKV was used for comparison. We quantified viral load in fetus and placentas and performed comprehensive gene expression profiling in the maternal (decidua) and fetal portion of placenta separately. Findings We demonstrate in a laboratory experimental setting that DENV can be transmitted vertically in a gestation stage-dependent manner similar to ZIKV, and this incidence drastically increases in the presence of enhancing antibodies. Interestingly, a high rate of DENV fetal infection occurs even though the placental viral load is significantly lower than that found in ZIKV-infected dams. Comprehensive gene expression profiling revealed DENV infection modulates a variety of inflammation-associated genes comparable to ZIKV in decidua and fetal placenta in early pregnancy. Interpretation Our findings suggest that the virus-induced modulation of host gene expression may facilitate DENV to cross the placental barrier in spite of lower viral burden compared to ZIKV. This mouse model may serve to identify the host determinants required for the vertical transmission of flaviviruses and develop appropriate countermeasures. Funding National Medical Research Council/Open Fund Individual Research Grant MOH-000524 (SW), MOH-000086 and OFIRG20nov-0017 (SGV).
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Affiliation(s)
- Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore.
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore
| | - Nicole Wei Wen Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore
| | | | - Avisha Chowdhury
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore
| | - Kenneth Tou En Chang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore; Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road 229899, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore; Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia.
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Hooda P, Ishtikhar M, Saraswat S, Bhatia P, Mishra D, Trivedi A, Kulandaisamy R, Aggarwal S, Munde M, Ali N, AlAsmari AF, Rauf MA, Inampudi KK, Sehgal D. Biochemical and Biophysical Characterisation of the Hepatitis E Virus Guanine-7-Methyltransferase. Molecules 2022; 27:1505. [PMID: 35268608 PMCID: PMC8911963 DOI: 10.3390/molecules27051505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatitis E virus (HEV) is an understudied pathogen that causes infection through fecal contaminated drinking water and is prominently found in South Asian countries. The virus affects ~20 million people annually, leading to ~60,000 infections per year. The positive-stranded RNA genome of the HEV genotype 1 has four conserved open reading frames (ORFs), of which ORF1 encodes a polyprotein of 180 kDa in size, which is processed into four non-structural enzymes: methyltransferase (MTase), papain-like cysteine protease, RNA-dependent RNA polymerase, and RNA helicase. MTase is known to methylate guanosine triphosphate at the 5'-end of viral RNA, thereby preventing its degradation by host nucleases. In the present study, we cloned, expressed, and purified MTase spanning 33-353 amino acids of HEV genotype 1. The activity of the purified enzyme and the conformational changes were established through biochemical and biophysical studies. The binding affinity of MTase with magnesium ions (Mg2+) was studied by isothermal calorimetry (ITC), microscale thermophoresis (MST), far-UV CD analysis and, fluorescence quenching. In summary, a short stretch of nucleotides has been cloned, coding for the HEV MTase of 37 kDa, which binds Mg2+ and modulate its activity. The chelation of magnesium reversed the changes, confirming its role in enzyme activity.
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Affiliation(s)
- Preeti Hooda
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, India; (P.H.); (M.I.); (S.S.); (P.B.); (D.M.); (A.T.)
| | - Mohd Ishtikhar
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, India; (P.H.); (M.I.); (S.S.); (P.B.); (D.M.); (A.T.)
| | - Shweta Saraswat
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, India; (P.H.); (M.I.); (S.S.); (P.B.); (D.M.); (A.T.)
| | - Pooja Bhatia
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, India; (P.H.); (M.I.); (S.S.); (P.B.); (D.M.); (A.T.)
| | - Deepali Mishra
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, India; (P.H.); (M.I.); (S.S.); (P.B.); (D.M.); (A.T.)
| | - Aditya Trivedi
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, India; (P.H.); (M.I.); (S.S.); (P.B.); (D.M.); (A.T.)
| | - Rajkumar Kulandaisamy
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India;
| | - Soumya Aggarwal
- School of Physical Sciences, Jawaharlal Nehru University (JNU), New Delhi 110067, India; (S.A.); (M.M.)
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University (JNU), New Delhi 110067, India; (S.A.); (M.M.)
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh 11451, Saudi Arabia; (N.A.); (A.F.A.)
| | - Abdullah F. AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh 11451, Saudi Arabia; (N.A.); (A.F.A.)
| | - Mohd A. Rauf
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48201, USA;
| | - Krishna K. Inampudi
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India;
| | - Deepak Sehgal
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, India; (P.H.); (M.I.); (S.S.); (P.B.); (D.M.); (A.T.)
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García-Ariza LL, Rocha-Roa C, Padilla-Sanabria L, Castaño-Osorio JC. Virtual Screening of Drug-Like Compounds as Potential Inhibitors of the Dengue Virus NS5 Protein. Front Chem 2022; 10:637266. [PMID: 35223766 PMCID: PMC8867075 DOI: 10.3389/fchem.2022.637266] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Dengue virus (DENV) is the causative agent of dengue fever. Annually, there are about 400 million new cases of dengue worldwide, and so far there is no specific treatment against this disease. The NS5 protein is the largest and most conserved viral protein among flaviviruses and is considered a therapeutic target of great interest. This study aims to search drug-like compounds for possible inhibitors of the NS5 protein in the four serotypes of DENV. Using a virtual screening from a ∼642,759-compound database, we suggest 18 compounds with NS5 binding and highlight the best compound per region, in the methyltransferase and RNA-dependent RNA polymerase domains. These compounds interact mainly with the amino acids of the catalytic sites and/or are involved in processes of protein activity. The identified compounds presented physicochemical and pharmacological properties of interest for their use as possible drugs; furthermore, we found that some of these compounds do not affect cell viability in Huh-7; therefore, we suggest evaluating these compounds in vitro as candidates in future research.
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Affiliation(s)
- Leidy L. García-Ariza
- Grupo de Inmunología Molecular, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
- *Correspondence: Leidy L. García-Ariza,
| | - Cristian Rocha-Roa
- Grupo de Parasitología Molecular, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
- Biophysics of Tropical Diseases, Max Planck Tandem Group, Universidad de Antioquia, Medellín, Colombia
| | - Leonardo Padilla-Sanabria
- Grupo de Inmunología Molecular, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| | - Jhon C. Castaño-Osorio
- Grupo de Inmunología Molecular, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
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Hashemian SMR, Pourhanifeh MH, Hamblin MR, Shahrzad MK, Mirzaei H. RdRp inhibitors and COVID-19: Is molnupiravir a good option? Biomed Pharmacother 2022; 146:112517. [PMID: 34902743 PMCID: PMC8654603 DOI: 10.1016/j.biopha.2021.112517] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Rapid changes in the viral genome allow viruses to evade threats posed by the host immune response or antiviral drugs, and can lead to viral persistence in the host cells. RNA-dependent RNA polymerase (RdRp) is an essential enzyme in RNA viruses, which is involved in RNA synthesis through the formation of phosphodiester bonds. Therefore, in RNA viral infections such as SARS-CoV-2, RdRp could be a crucial therapeutic target. The present review discusses the promising application of RdRp inhibitors, previously approved or currently being tested in human clinical trials, in the treatment of RNA virus infections. Nucleoside inhibitors (NIs) bind to the active site of RdRp, while nonnucleoside inhibitors (NNIs) bind to allosteric sites. Given the absence of highly effective drugs for the treatment of COVID-19, the discovery of an efficient treatment for this pandemic is an urgent concern for researchers around the world. We review the evidence for molnupiravir (MK-4482, EIDD-2801), an antiviral drug originally designed for Alphavirus infections, as a potential preventive and therapeutic agent for the management of COVID-19. At the beginning of this pandemic, molnupiravir was in preclinical development for seasonal influenza. When COVID-19 spread dramatically, the timeline for development was accelerated to focus on the treatment of this pandemic. Real time consultation with regulators took place to expedite this program. We summarize the therapeutic potential of RdRp inhibitors, and highlight molnupiravir as a new small molecule drug for COVID-19 treatment.
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Affiliation(s)
- Seyed Mohammad Reza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Mohammad Karim Shahrzad
- Department of Internal Medicine and Endocrinology, ShohadaeTajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hamed Mirzaei
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran; Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, IR, Iran.
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Wang S, Chan KWK, Tan MJA, Flory C, Luo D, Lescar J, Forwood JK, Vasudevan SG. A conserved arginine in NS5 binds genomic 3' stem-loop RNA for primer-independent initiation of flavivirus RNA replication. RNA (NEW YORK, N.Y.) 2022; 28:177-193. [PMID: 34759006 PMCID: PMC8906541 DOI: 10.1261/rna.078949.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The commitment to replicate the RNA genome of flaviviruses without a primer involves RNA-protein interactions that have been shown to include the recognition of the stem-loop A (SLA) in the 5' untranslated region (UTR) by the nonstructural protein NS5. We show that DENV2 NS5 arginine 888, located within the carboxy-terminal 18 residues, is completely conserved in all flaviviruses and interacts specifically with the top-loop of 3'SL in the 3'UTR which contains the pentanucleotide 5'-CACAG-3' previously shown to be critical for flavivirus RNA replication. We present virological and biochemical data showing the importance of this Arg 888 in virus viability and de novo initiation of RNA polymerase activity in vitro. Based on our binding studies, we hypothesize that ternary complex formation of NS5 with 3'SL, followed by dimerization, leads to the formation of the de novo initiation complex that could be regulated by the reversible zipping and unzipping of cis-acting RNA elements.
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Affiliation(s)
- Sai Wang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Min Jie Alvin Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Charlotte Flory
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 636921 Singapore
| | - Julian Lescar
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
- Department of Microbiology and Immunology, National University of Singapore, 117545 Singapore
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia
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Gharbi-Ayachi A, El Sahili A, Lescar J. Purification of Dengue and Zika Virus Non-structural Protein 5 for Crystallization and Screening of Antivirals. Methods Mol Biol 2022; 2409:47-61. [PMID: 34709635 DOI: 10.1007/978-1-0716-1879-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dengue Virus (DENV) and ZIKA Virus (ZIKV) are two important human pathogens that belong to the Flavivirus genus of positive strand RNA viruses. Symptoms of DENV infections range from asymptomatic or mild fever to life-threatening forms, while ZIKV can lead to teratogenic effects such as microcephaly in newborns and neurological disease like the Guillain-Barré syndrome.Non-Structural Protein 5 (NS5) is the largest and most conserved enzyme across flaviviruses and hence constitutes a prime target for developing pan-flavivirus antiviral inhibitors. NS5 results from the gene fusion between a methyltransferase at the N-terminus of the protein and an RNA-dependent RNA polymerase (RdRp) at the C-terminal end. The NS5 protein plays key roles in replication and modification of viral RNA and its inhibition by potent antiviral drugs could prevent severe symptoms associated with infections.We have optimized purification and crystallization protocols to obtain active recombinant proteins suitable for structure-based drug discovery for both the full-length NS5 protein and the polymerase domain of NS5 from DENV and ZIKV .
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Affiliation(s)
- Aicha Gharbi-Ayachi
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
| | - Abbas El Sahili
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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Cheng CX, Alvin Tan MJ, Chan KWK, Watanabe S, Wang S, Choy MM, Manuel M, Victorio CBL, Ong J, Reolo M, Chacko AM, Vasudevan SG. In Vitro and In Vivo Stability of P884T, a Mutation that Relocalizes Dengue Virus 2 Non-structural Protein 5. ACS Infect Dis 2021; 7:3277-3291. [PMID: 34735113 DOI: 10.1021/acsinfecdis.1c00441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dengue virus (DENV) non-structural protein 5 (NS5) is critical for viral RNA synthesis within endoplasmic reticulum (ER)-derived replication complexes in the cytoplasm; however a proportion of NS5 is known to be localized to the nucleus of infected cells. The importance of nuclear DENV NS5 on viral replication and pathogenesis is still unclear. We recently discovered a nuclear localization signal (NLS) residing in the C-terminal 18 amino acid (Cter18) region of DENV NS5 and that a single NS5 P884T amino acid substitution adjacent to the NLS is sufficient to relocalize a significant proportion of DENV2 NS5 from the nucleus to the cytoplasm of infected cells. Here, in vitro studies show that the DENV2 NS5 P884T mutant replicates similarly to the parental wild-type infectious clone-derived virus while inducing a greater type I interferon and inflammatory cytokine response, in a manner independent of NS5's ability to degrade STAT2 or regulate SAT1 splicing. In both AG129 mouse and Aedes aegypti mosquito infection models, the P884T virus exhibits lower levels of viral replication only at early timepoints. Intriguingly, there appears to be a tendency for selection pressure to revert to the wild-type proline in P884T-infected Ae. aegypti, in agreement with the high conservation of the proline at this position of NS5 in DENV2, 3, and 4. These results suggest that the predominant nuclear localization of DENV NS5, while not required for viral RNA replication, may play a role in pathogenesis and modulation of the host immune response and contribute to viral fitness in the mosquito host.
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Affiliation(s)
- Colin X. Cheng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Min Jie Alvin Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Kitti W. K. Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Satoru Watanabe
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sai Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Milly M. Choy
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Menchie Manuel
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Carla B. L. Victorio
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Joanne Ong
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Marie Reolo
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ann-Marie Chacko
- Laboratory for Translational and Molecular Imaging, Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Subhash G. Vasudevan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, NUS, 5 Science Drive 2, Singapore 117545, Singapore
- Institute for Glycomics, Griffith University, Southport 4222, Australia
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Khan RA, Hossain R, Siyadatpanah A, Al-Khafaji K, Khalipha ABR, Dey D, Asha UH, Biswas P, Saikat ASM, Chenari HA, Wilairatana P, Islam MT. Diterpenes/Diterpenoids and Their Derivatives as Potential Bioactive Leads against Dengue Virus: A Computational and Network Pharmacology Study. Molecules 2021; 26:6821. [PMID: 34833913 PMCID: PMC8623982 DOI: 10.3390/molecules26226821] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
Dengue fever is a dangerous infectious endemic disease that affects over 100 nations worldwide, from Africa to the Western Pacific, and is caused by the dengue virus, which is transmitted to humans by an insect bite of Aedes aegypti. Millions of citizens have died as a result of dengue fever and dengue hemorrhagic fever across the globe. Envelope (E), serine protease (NS3), RNA-directed RNA polymerase (NS5), and non-structural protein 1 (NS1) are mostly required for cell proliferation and survival. Some of the diterpenoids and their derivatives produced by nature possess anti-dengue viral properties. The goal of the computational study was to scrutinize the effectiveness of diterpenoids and their derivatives against dengue viral proteins through in silico study. Methods: molecular docking was performed to analyze the binding affinity of compounds against four viral proteins: the envelope (E) protein, the NS1 protein, the NS3 protein, and the NS5 protein. Results: among the selected drug candidates, triptolide, stevioside, alepterolic acid, sphaeropsidin A, methyl dodovisate A, andrographolide, caesalacetal, and pyrimethamine have demonstrated moderate to good binding affinities (-8.0 to -9.4 kcal/mol) toward the selected proteins: E protein, NS3, NS5, and NS1 whereas pyrimethamine exerts -7.5, -6.3, -7.8, and -6.6 kcal/mol with viral proteins, respectively. Interestingly, the binding affinities of these lead compounds were better than those of an FDA-approved anti-viral medication (pyrimethamine), which is underused in dengue fever. Conclusion: we can conclude that diterpenoids can be considered as a possible anti-dengue medication option. However, in vivo investigation is recommended to back up the conclusions of this study.
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Affiliation(s)
- Rasel Ahmed Khan
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9280, Bangladesh;
| | - Rajib Hossain
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 9717853577, Iran; (A.S.); (H.A.C.)
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, Al-Nisour University College, Baghdad 10001, Iraq;
| | - Abul Bashar Ripon Khalipha
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (D.D.); (A.S.M.S.)
| | - Umma Hafsa Asha
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh;
| | - Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (D.D.); (A.S.M.S.)
| | - Hadi Ahmadi Chenari
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 9717853577, Iran; (A.S.); (H.A.C.)
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
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In Silico Analysis of Dengue Virus Serotype 2 Mutations Detected at the Intrahost Level in Patients with Different Clinical Outcomes. Microbiol Spectr 2021; 9:e0025621. [PMID: 34468189 PMCID: PMC8557815 DOI: 10.1128/spectrum.00256-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Intrahost genetic diversity is thought to facilitate arbovirus adaptation to changing environments and hosts, and it may also be linked to viral pathogenesis. Intending to shed light on the viral determinants for severe dengue pathogenesis, we previously analyzed the DENV-2 intrahost genetic diversity in 68 patients clinically classified as dengue fever (n = 31), dengue with warning signs (n = 19), and severe dengue (n = 18), performing viral whole-genome deep sequencing from clinical samples with an amplicon-free approach. From it, we identified a set of 141 relevant mutations distributed throughout the viral genome that deserved further attention. Therefore, we employed molecular modeling to recreate three-dimensional models of the viral proteins and secondary RNA structures to map the mutations and assess their potential effects. Results showed that, in general lines, disruptive variants were identified primarily among dengue fever cases. In contrast, potential immune-escape variants were associated mainly with warning signs and severe cases, in line with the latter's longer intrahost evolution times. Furthermore, several mutations were located on protein-surface regions, with no associated function. They could represent sites of further investigation, as the interaction of viral and host proteins is critical for both host immunomodulation and virus hijacking of the cellular machinery. The present analysis provides new information about the implications of the intrahost genetic diversity of DENV-2, contributing to the knowledge about the viral factors possibly involved in its pathogenesis within the human host. Strengthening our results with functional studies could allow many of these variants to be considered in the design of therapeutic or prophylactic compounds and the improvement of diagnostic assays. IMPORTANCE Previous evidence showed that intrahost genetic diversity in arboviruses may be linked to viral pathogenesis and that one or a few amino acid replacements within a single protein are enough to modify a biological feature of an RNA virus. To assess dengue virus serotype 2 determinants potentially involved in pathogenesis, we previously analyzed the intrahost genetic diversity of the virus in patients with different clinical outcomes and identified a set of 141 mutations that deserved further study. Thus, through a molecular modeling approach, we showed that disruptive variants were identified primarily among cases with mild dengue fever, while potential immune-escape variants were mainly associated with cases of greater severity. We believe that some of the variants pointed out in this study were attractive enough to be potentially considered in future intelligent designs of therapeutic or prophylactic compounds or the improvement of diagnostic tools. The present analysis provides new information about DENV-2 viral factors possibly involved in its pathogenesis within the human host.
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Optimal flexibility of the linker region of Zika virus NS5 methyltransferase-polymerase is critical for virus replication. Antiviral Res 2021; 195:105194. [PMID: 34699863 DOI: 10.1016/j.antiviral.2021.105194] [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: 09/20/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022]
Abstract
The flavivirus NS5 protein contains an N-terminal methyl-transferase (MTase) connected through a flexible linker with a C-terminal RNA-dependent RNA-polymerase (RdRp) domain, that work cooperatively to replicate and methylate the viral genome. In this study we probed the importance of an evolutionary-conserved hydrophobic residue (Val266) located at the start of the ten-residue interdomain linker of Zika virus (ZIKV) NS5. In flavivirus NS5 crystal structures, the start of the linker forms a 310 helix when NS5 adopts a compact conformation, but becomes disordered or extended in open conformations. Using reverse genetics system, we either introduced rigidity in the linker through mutation to a proline or flexibility through a glycine mutation at position 266. ZIKV NS5 Val 266 to Pro mutation was lethal for viral RNA replication while the Gly mutation was severely attenuated. Serial passaging of cell culture supernatant derived from C6/36 mosquito cells transfected with mutant ZIKV RNA showed that the attenuation can be rescued. Next generation deep sequencing revealed four single nucleotide polymorphisms that occur with an allele frequency >98%. The single non-synonymous NS5 mutation Glu419 to Lys is adjacent to RdRp motif G at the tip of the fingers subdomain, while the remaining three are synonymous variants at nucleotide positions 1403, 4403 and 6653 in the genome. Reverse engineering the changes into the ZIKV NS5/Val266Gly background followed by serial passaging revealed that residue 266 is under strong positive selection to revert back to Val. The interaction of the specific conformation of the NS5 linker with Val at position 266 and the RNA binding motif G region may present a potential strategy for allosteric antiviral drug development.
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Current Trends and Limitations in Dengue Antiviral Research. Trop Med Infect Dis 2021; 6:tropicalmed6040180. [PMID: 34698303 PMCID: PMC8544673 DOI: 10.3390/tropicalmed6040180] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
Dengue is the most prevalent arthropod-borne viral disease worldwide and affects approximately 2.5 billion people living in over 100 countries. Increasing geographic expansion of Aedes aegypti mosquitoes (which transmit the virus) has made dengue a global health concern. There are currently no approved antivirals available to treat dengue, and the only approved vaccine used in some countries is limited to seropositive patients. Treatment of dengue, therefore, remains largely supportive to date; hence, research efforts are being intensified for the development of antivirals. The nonstructural proteins, 3 and 5 (NS3 and NS5), have been the major targets for dengue antiviral development due to their indispensable enzymatic and biological functions in the viral replication process. NS5 is the largest and most conserved nonstructural protein encoded by flaviviruses. Its multifunctionality makes it an attractive target for antiviral development, but research efforts have, this far, not resulted in the successful development of an antiviral targeting NS5. Increase in structural insights into the dengue NS5 protein will accelerate drug discovery efforts focused on NS5 as an antiviral target. In this review, we will give an overview of the current state of therapeutic development, with a focus on NS5 as a therapeutic target against dengue.
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Fernandes PO, Chagas MA, Rocha WR, Moraes AH. Non-structural protein 5 (NS5) as a target for antiviral development against established and emergent flaviviruses. Curr Opin Virol 2021; 50:30-39. [PMID: 34340199 DOI: 10.1016/j.coviro.2021.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 11/19/2022]
Abstract
Flaviviruses are among the most critical pathogens in tropical regions and cause a growing number of severe diseases in developing countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Among the ten proteins encoded in the flavivirus RNA, non-structural protein 5, NS5, is a promising drug target. NS5 plays a fundamental role in flavivirus replication, viral RNA methylation, RNA polymerization, and host immune system evasion. Most of the NS5 inhibitor candidates target NS5 active sites. However, the similarity of NS5 activity sites with human enzymes can cause side effects. Identifying new allosteric sites in NS5 can contribute enormously to antiviral development. The NS5 structural characterization enabled exploring new regions, such as the residues involved in MTase-RdRp interaction, NS5 oligomerization, and NS5 interaction with other viral and host-cell proteins. Targeting NS5 critical interactions might lead to new compounds and overcomes the toxicity of current NS5-inhibitor candidates.
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Affiliation(s)
- Philipe O Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Marcelo A Chagas
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Willian R Rocha
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil; Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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Bhatia S, Narayanan N, Nagpal S, Nair DT. Antiviral therapeutics directed against RNA dependent RNA polymerases from positive-sense viruses. Mol Aspects Med 2021; 81:101005. [PMID: 34311994 DOI: 10.1016/j.mam.2021.101005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/18/2023]
Abstract
Viruses with positive-sense single stranded RNA (+ssRNA) genomes are responsible for different diseases and represent a global health problem. In addition to developing new vaccines that protect against severe illness on infection, it is imperative to identify new antiviral molecules to treat infected patients. The genome of these RNA viruses generally codes for an enzyme with RNA dependent RNA polymerase (RdRP) activity. This molecule is centrally involved in the duplication of the RNA genome. Inhibition of this enzyme by small molecules will prevent duplication of the RNA genome and thus reduce the viral titer. An overview of the different therapeutic strategies used to inhibit RdRPs from +ssRNA viruses is provided, along with an analysis of these enzymes to highlight new binding sites for inhibitors.
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Affiliation(s)
- Sonam Bhatia
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Shilpi Nagpal
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India.
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Gong P. Structural basis of viral RNA-dependent RNA polymerase nucleotide addition cycle in picornaviruses. Enzymes 2021; 49:215-233. [PMID: 34696833 DOI: 10.1016/bs.enz.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of processive nucleic acid polymerases, carrying out DNA-independent replication/transcription processes. Although viral RdRPs have versatile global structures, they do share a structurally highly conserved active site comprising catalytic motifs A-G. In spite of different initiation modes, the nucleotide addition cycle (NAC) in the RdRP elongation phase probably follows consistent mechanisms. In this chapter, representative structures of picornavirus RdRP elongation complexes are used to illustrate RdRP NAC mechanisms. In the pre-chemistry part of the NAC, RdRPs utilize a unique palm domain-based active site closure that can be further decomposed into two sequential steps. In the post-chemistry part of the NAC, the translocation process is stringently controlled by the RdRP-specific motif G, resulting in asymmetric movements of the template-product RNA. Future efforts to elucidate regulation/intervention mechanisms by mismatched NTPs or nucleotide analog antivirals are necessary to achieve comprehensive understandings of viral RdRP NAC.
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Affiliation(s)
- Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China.
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Insights on Dengue and Zika NS5 RNA-dependent RNA polymerase (RdRp) inhibitors. Eur J Med Chem 2021; 224:113698. [PMID: 34274831 DOI: 10.1016/j.ejmech.2021.113698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 11/20/2022]
Abstract
Over recent years, many outbreaks caused by (re)emerging RNA viruses have been reported worldwide, including life-threatening Flaviviruses, such as Dengue (DENV) and Zika (ZIKV). Currently, there is only one licensed vaccine against Dengue, Dengvaxia®. However, its administration is not recommended for children under nine years. Still, there are no specific inhibitors available to treat these infectious diseases. Among the flaviviral proteins, NS5 RNA-dependent RNA polymerase (RdRp) is a metalloenzyme essential for viral replication, suggesting that it is a promising macromolecular target since it has no human homolog. Nowadays, several NS5 RdRp inhibitors have been reported, while none inhibitors are currently in clinical development. In this context, this review constitutes a comprehensive work focused on RdRp inhibitors from natural, synthetic, and even repurposing sources. Furthermore, their main aspects associated with the structure-activity relationship (SAR), proposed mechanisms of action, computational studies, and other topics will be discussed in detail.
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50
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Diakou KI, Mitsis T, Pierouli K, Papakonstantinou E, Megalooikonomou V, Efthimiadou A, Vlachakis D. Study of the Langat virus RNA-dependent RNA polymerase through homology modeling. ACTA ACUST UNITED AC 2021; 26. [PMID: 34316455 PMCID: PMC8312719 DOI: 10.14806/ej.26.1.944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Langat virus is a member of the Flaviviridae family and a close relative of a group of important tick-borne viruses that cause human encephalitis. RNA-dependent RNA polymerase is a significant component of the replication mechanism of the Flaviviridae viral family. In the present work, a three-dimensional model of the Langat virus RNA-dependent RNA polymerase was designed through homology modeling. The experimentally determined structure of the RNA-dependent RNA polymerase of Dengue virus type II, another member of the same viral family, was employed as template for the homology modeling process. The resulting model underwent a series of optimisations and its quality was verified using the Verify3D algorithm. Important functional characteristics of the family of viral RNA-dependent RNA polymerases were identified in the generated model, thus affirming the potential for its use in the possible design of anti-viral agents for Langat virus.
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Affiliation(s)
- Kalliopi Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Vasileios Megalooikonomou
- Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Aspasia Efthimiadou
- Department of Soil Science of Athens, Institute of Soil and Water Resources, Hellenic Agricultural Organization - Demeter, Attica, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.,Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
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