1
|
Sharma P, Moustafa M, Al-Shehri M, Alotaibi F, Bhardwaj R, Singh IK. A simulation-based approach to target Zika virus RNA-dependent RNA polymerase with marine compounds for antiviral development. J Biomol Struct Dyn 2024:1-11. [PMID: 38415996 DOI: 10.1080/07391102.2024.2322620] [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: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
Despite significant efforts, currently, there is no particular drug available to treat Zika virus (ZIKV) infection, highlighting the urgent need for effective therapeutic interventions. To identify putative inhibitors of the ZIKV RdRp protein's RNA binding function, the present study applied an extensive in-silico drug discovery methodology. The initial phase involved virtual screening using Lipinski's rule of five as a filter, ensuring the selection of molecules with favorable pharmacokinetic properties. This process yielded 238 compounds with promising docking scores, ranging from -6.0 to -7.48 kcal/mol, indicative of their potential binding affinity to the ZIKV RdRp. To refine the selection, these compounds underwent a re-docking process, comparing their binding energies with a reference molecule known for its inhibitory action against RdRp. Remarkably, five compounds, labeled CMNPD30598, CMNPD27464, CMNPD25971, CMNPD27444, and CMNPD16599, demonstrated superior re-docking energies compared to the reference, suggesting a stronger interaction with the RdRp allosteric site. Subsequent molecular dynamics (MD) simulations provided insights into the stability of these complexes over time, reinforcing their potential as RdRp inhibitors. Additionally, the calculation of free binding energies and principal component analysis (PCA) of the free energy landscape offered a deeper understanding of the binding dynamics and energetics. This study not only highlights the utility of marine fungi compounds in antiviral drug discovery but also showcases the power of computational tools in identifying novel therapeutics. The identified compounds represent promising candidates for further experimental validation and development as ZIKV RdRp inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mahmoud Moustafa
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammed Al-Shehri
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Faisal Alotaibi
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Shaqraa, Saudi Arabia
| | - Rima Bhardwaj
- Department of Chemistry, Poona College, Savitribai Phule Pune University, Pune, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| |
Collapse
|
2
|
Zhang K, Liang J, Zhang B, Huang L, Yu J, Xiao X, He Z, Tao H, Yuan J. A Marine Natural Product, Harzianopyridone, as an Anti-ZIKV Agent by Targeting RNA-Dependent RNA Polymerase. Molecules 2024; 29:978. [PMID: 38474490 DOI: 10.3390/molecules29050978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The Zika virus (ZIKV) is a mosquito-borne virus that already poses a danger to worldwide human health. Patients infected with ZIKV generally have mild symptoms like a low-grade fever and joint pain. However, severe symptoms can also occur, such as Guillain-Barré syndrome, neuropathy, and myelitis. Pregnant women infected with ZIKV may also cause microcephaly in newborns. To date, we still lack conventional antiviral drugs to treat ZIKV infections. Marine natural products have novel structures and diverse biological activities. They have been discovered to have antibacterial, antiviral, anticancer, and other therapeutic effects. Therefore, marine products are important resources for compounds for innovative medicines. In this study, we identified a marine natural product, harzianopyridone (HAR), that could inhibit ZIKV replication with EC50 values from 0.46 to 2.63 µM while not showing obvious cytotoxicity in multiple cellular models (CC50 > 45 µM). Further, it also reduced the expression of viral proteins and protected cells from viral infection. More importantly, we found that HAR directly bound to the ZIKV RNA-dependent RNA polymerase (RdRp) and suppressed its polymerase activity. Collectively, our findings provide HAR as an option for the development of anti-ZIKV drugs.
Collapse
Affiliation(s)
- Kexin Zhang
- 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
| | - Jingyao 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
| | - Bingzhi Zhang
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lishan Huang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jianchen Yu
- 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
| | - Xuhan Xiao
- 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
| | - 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
| | - Huaming Tao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, 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
| |
Collapse
|
3
|
Wang L, Zhou R, Liu Y, Guo S, Yi D, Zhao J, Li Q, Zhang Y, Liang C, Wang J, Shan G, Cen S. A cell-based assay to discover inhibitors of Zika virus RNA-dependent RNA polymerase. Virology 2024; 589:109939. [PMID: 37979208 DOI: 10.1016/j.virol.2023.109939] [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: 09/19/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Zika virus (ZIKV) belongs to Flaviviridae, the Flavivirus genus. Its infection causes congenital brain abnormalities and Guillain-Barré syndrome. However, there are no effective vaccines, no FDA-approved drugs to manage ZIKV infection. The non-structural protein NS5 of ZIKV has been recognized as a valuable target of antivirals because of its RNA-dependent RNA polymerase (RdRp) and methyltransferase (MTase) activities essential for viral RNA synthesis. Here, we report a cell-based assay for discovering inhibitors of ZIKV NS5 and found that 5-Azacytidine potently inhibits ZIKV NS5, with EC50 of 4.9 μM. Furthermore, 5-Azacytidine suppresses ZIKV replication by inhibiting NS5-mediated viral RNA transcription. Therefore, we have developed a cell-based ZIKV NS5 assay which can be deployed to discover ZIKV NS5 inhibitors and demonstrated the potential of 5-Azacytidine for further development as a ZIKV NS5 inhibitor.
Collapse
Affiliation(s)
- Lidan Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Rui Zhou
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Yitong Liu
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Saisai Guo
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Dongrong Yi
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Jianyuan Zhao
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Quanjie Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Yongxin Zhang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China
| | - Chen Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, H3T 1E2, Canada
| | - Jing Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China.
| | - Guangzhi Shan
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China.
| | - Shan Cen
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantanxili, Beijing, 100050, China.
| |
Collapse
|
4
|
Patar AK, Borah SM, Barman J, Bora A, Baruah TJ. Dronabinol as an answer to flavivirus infections: an in-silico investigation. J Biomol Struct Dyn 2023; 41:11219-11230. [PMID: 36576139 DOI: 10.1080/07391102.2022.2160817] [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: 09/23/2021] [Accepted: 12/15/2022] [Indexed: 12/29/2022]
Abstract
Flavivirus infections are common in several parts of the world. Two major types of flaviviruses are dengue and zika viruses. Both these two viral infections have caused many fatalities around the world. There is an absence of a vaccine and an effective medication against these viruses. In this study, we analyzed the ability of dronabinol to act as a potential cure against these viral infections. We performed the docking of dronabinol with several viral proteins followed by molecular dynamics simulation, MM/PBSA and PCA analysis. We checked the ability of the polyphenol dronabinol to interfere with the binding of viral helicases to their cellular targets. We performed 2 D-QSAR studies, drug likeliness, ADMET and target prediction studies. From our study, we observed that dronabinol had the best docking ability against the helicase proteins of dengue and zika. Molecular dynamics simulation and MM/PBSA investigation confirmed the stability of the binding while PCA investigation showed a lowering of molecular motions in response to dronabinol docking to the helicases. Dronabinol interfered in the binding of the helicases to RNA. 2 D QSAR studies revealed a low IC50 value for dronabinol. Dronabinol showed favorable drug-likeness, ADMET properties and target prediction results. Thus we propose dronabinol be further investigated in-vitro as a cure against dengue and zika virus infections.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abani Kumar Patar
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Sapna Mayuri Borah
- Department of Plant Pathology, Assam Agricultural University, Jorhat, Assam, India
| | - Jitul Barman
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Anupam Bora
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| | - Taranga Jyoti Baruah
- Department of Biochemistry, Assam Royal Global University, Guwahati, Assam, India
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Chen R, Francese R, Wang N, Li F, Sun X, Xu B, Liu J, Liu Z, Donalisio M, Lembo D, Zhou GC. Exploration of novel hexahydropyrrolo[1,2-e]imidazol-1-one derivatives as antiviral agents against ZIKV and USUV. Eur J Med Chem 2023; 248:115081. [PMID: 36623328 DOI: 10.1016/j.ejmech.2022.115081] [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: 10/20/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Zika virus (ZIKV) and Usutu virus (USUV) are two emerging flaviviruses mostly transmitted by mosquitos. ZIKV is associated with microcephaly in newborns and the less-known USUV, with its reported neurotropism and its extensive spread in Europe, represents a growing concern for human health. There is still no approved vaccine or specific antiviral against ZIKV and USUV infections. The main goal of this study is to investigate the anti-ZIKV and anti-USUV activity of a new library of compounds and to preliminarily investigate the mechanism of action of the selected hit compounds in vitro. Two potent anti-ZIKV and anti-USUV agents, namely ZDL-115 and ZDL-116, were discovered, both presenting low cytotoxicity, cell-line independent antiviral activity in the low micromolar range and ability of reducing viral progeny production. The analysis of the structure-activity relationship (SAR) revealed that introduction of 2-deoxyribose to 3-arene was fundamental to enhance the solubility and improve the antiviral action. Additionally, we demonstrated that ZDL-115 and ZDL-116 are significantly active against both viruses when added on cells for at least 24 h prior to viral inoculation or immediately post-infection. The docking analysis showed that ZDL-116 could target the host vitamin D receptor (VDR) and viral proteins. Future experiments will be focused on compound modification to discover analogues that are more potent and on the clarification of the mechanism of action and the specific drug target. The discovery and the development of a novel anti-flavivirus drug will have a significant impact in a context where there are no fully effective antiviral drugs or vaccines for most flaviviruses.
Collapse
Affiliation(s)
- Ran Chen
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China; Xitaihu Lake Industrial College, Nanjing Tech University, Changzhou, 213149, Jiangsu, China
| | - Rachele Francese
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy
| | - Na Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Feng Li
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xia Sun
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Bin Xu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Jinsong Liu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhuyun Liu
- School of Pharmacy, Taizhou Polytechnic College, Taizhou, 225300, Jiangsu, China
| | - Manuela Donalisio
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy
| | - David Lembo
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy.
| | - Guo-Chun Zhou
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China; Xitaihu Lake Industrial College, Nanjing Tech University, Changzhou, 213149, Jiangsu, China.
| |
Collapse
|
7
|
Chen Y, Chi X, Zhang H, Zhang Y, Qiao L, Ding J, Han Y, Lin Y, Jiang J. Identification of Potent Zika Virus NS5 RNA-Dependent RNA Polymerase Inhibitors Combining Virtual Screening and Biological Assays. Int J Mol Sci 2023; 24:ijms24031900. [PMID: 36768218 PMCID: PMC9915956 DOI: 10.3390/ijms24031900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
The Zika virus (ZIKV) epidemic poses a significant threat to human health globally. Thus, there is an urgent need for developing effective anti-ZIKV agents. ZIKV non-structural protein 5 RNA-dependent RNA polymerase (RdRp), a viral enzyme for viral replication, has been considered an attractive drug target. In this work, we screened an anti-infection compound library and a natural product library by virtual screening to identify potential candidates targeting RdRp. Then, five selected candidates were further applied for RdRp enzymatic analysis, cytotoxicity, and binding examination by SPR. Finally, posaconazole (POS) was confirmed to effectively inhibit both RdRp activity with an IC50 of 4.29 μM and the ZIKV replication with an EC50 of 0.59 μM. Moreover, POS was shown to reduce RdRp activity by binding with the key amino acid D666 through molecular docking and site-directed mutation analysis. For the first time, our work found that POS could inhibit ZIKV replication with a stronger inhibitory activity than chloroquine. This work also demonstrated fast anti-ZIKV screening for inhibitors of RdRp and provided POS as a potential anti-ZIKV agent.
Collapse
|
8
|
Mottin M, de Paula Sousa BK, de Moraes Roso Mesquita NC, de Oliveira KIZ, Noske GD, Sartori GR, de Oliveira Albuquerque A, Urbina F, Puhl AC, Moreira-Filho JT, Souza GE, Guido RV, Muratov E, Neves BJ, da Silva JHM, Clark AE, Siqueira-Neto JL, Perryman AL, Oliva G, Ekins S, Andrade CH. Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. J Chem Inf Model 2022; 62:6825-6843. [PMID: 36239304 PMCID: PMC9923514 DOI: 10.1021/acs.jcim.2c00596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Zika virus (ZIKV) is a neurotropic arbovirus considered a global threat to public health. Although there have been several efforts in drug discovery projects for ZIKV in recent years, there are still no antiviral drugs approved to date. Here, we describe the results of a global collaborative crowdsourced open science project, the OpenZika project, from IBM's World Community Grid (WCG), which integrates different computational and experimental strategies for advancing a drug candidate for ZIKV. Initially, molecular docking protocols were developed to identify potential inhibitors of ZIKV NS5 RNA-dependent RNA polymerase (NS5 RdRp), NS3 protease (NS2B-NS3pro), and NS3 helicase (NS3hel). Then, a machine learning (ML) model was built to distinguish active vs inactive compounds for the cytoprotective effect against ZIKV infection. We performed three independent target-based virtual screening campaigns (NS5 RdRp, NS2B-NS3pro, and NS3hel), followed by predictions by the ML model and other filters, and prioritized a total of 61 compounds for further testing in enzymatic and phenotypic assays. This yielded five non-nucleoside compounds which showed inhibitory activity against ZIKV NS5 RdRp in enzymatic assays (IC50 range from 0.61 to 17 μM). Two compounds thermally destabilized NS3hel and showed binding affinity in the micromolar range (Kd range from 9 to 35 μM). Moreover, the compounds LabMol-301 inhibited both NS5 RdRp and NS2B-NS3pro (IC50 of 0.8 and 7.4 μM, respectively) and LabMol-212 thermally destabilized the ZIKV NS3hel (Kd of 35 μM). Both also protected cells from death induced by ZIKV infection in in vitro cell-based assays. However, while eight compounds (including LabMol-301 and LabMol-212) showed a cytoprotective effect and prevented ZIKV-induced cell death, agreeing with our ML model for prediction of this cytoprotective effect, no compound showed a direct antiviral effect against ZIKV. Thus, the new scaffolds discovered here are promising hits for future structural optimization and for advancing the discovery of further drug candidates for ZIKV. Furthermore, this work has demonstrated the importance of the integration of computational and experimental approaches, as well as the potential of large-scale collaborative networks to advance drug discovery projects for neglected diseases and emerging viruses, despite the lack of available direct antiviral activity and cytoprotective effect data, that reflects on the assertiveness of the computational predictions. The importance of these efforts rests with the need to be prepared for future viral epidemic and pandemic outbreaks.
Collapse
Affiliation(s)
- Melina Mottin
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia, 70910-900, Brazil
| | - Bruna Katiele de Paula Sousa
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | | | | | - Gabriela Dias Noske
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | | | | | - Fabio Urbina
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, 27606, USA
| | - Ana C. Puhl
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, 27606, USA
| | - José Teófilo Moreira-Filho
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | - Guilherme E. Souza
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | - Rafael V.C. Guido
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | - Eugene Muratov
- University of North Carolina - University of North Carolina at Chapel Hill, 27599, USA
- Universidade Federal de Paraíba, Joao Pessoa, PB, 58051-900, Brazil
| | - Bruno Junior Neves
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | | | - Alex E. Clark
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, USA
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, 92093, USA
| | - Alexander L. Perryman
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University–New Jersey Medical School, Newark, NJ 07103, United States
- Repare Therapeutics, 7210 Rue Frederick-Banting, Suite 100, Montreal, QC, H4S 2A1, Canada
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Avenida João Dagnone, 1100, São Carlos, São Paulo, 13563-120, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, 27606, USA
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| |
Collapse
|
9
|
Sharma PP, Kumar S, Srivastava S, Srivastava M, Jee B, Gorobets NY, Kumar D, Kumar M, Asthana S, Zhang P, Poonam, Zoltner M, Rathi B. Computational study of novel inhibitory molecule, 1-(4-((2 S,3 S)-3-amino-2-hydroxy-4-phenylbutyl)piperazin-1-yl)-3-phenylurea, with high potential to competitively block ATP binding to the RNA dependent RNA polymerase of SARS-CoV-2 virus. J Biomol Struct Dyn 2022; 40:10162-10180. [PMID: 34151735 DOI: 10.1080/07391102.2021.1940281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
For coronaviruses, RNA-dependent RNA polymerase (RdRp) is an essential enzyme that catalyses the replication from RNA template and therefore remains an attractive therapeutic target for anti-COVID drug discovery. In the present study, we performed a comprehensive in silico screening for 16,776 potential molecules from recently established drug libraries based on two important pharmacophores (3-amino-4-phenylbutan-2-ol and piperazine). Based on initial assessment, 4042 molecules were obtained suitable as drug candidates, which were following Lipinski's rule. Molecular docking implemented for the analysis of molecular interactions narrowed this number of compounds down to 19. Subsequent to screening filtering criteria and considering the critical parameters viz. docking score and MM-GBSA binding free energy, 1-(4-((2S,3S)-3-amino-2-hydroxy-4-phenylbutyl)piperazin-1-yl)-3-phenylurea (compound 1) was accomplished to score highest in comparison to the remaining 18 shortlisted drug candidates. Notably, compound 1 displayed higher docking score (-8.069 kcal/mol) and MM-GBSA binding free energy (-49.56 kcal/mol) than the control drug, remdesivir triphosphate, the active form of remdesivir as well as adenosine triphosphate. Furthermore, a molecular dynamics simulation was carried out (100 ns), which substantiated the candidacy of compound 1 as better inhibitor. Overall, our systematic in silico study predicts the potential of compound 1 to exhibit a more favourable specific activity than remdesivir triphosphate. Hence, we suggest compound 1 as a novel potential drug candidate, which should be considered for further exploration and validation of its potential against SARS-CoV-2 in wet lab experimental studies.Communicated by Ramasawamy H. Sarma.
Collapse
Affiliation(s)
- Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Sukrit Srivastava
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India.,Infection Biology Group, Indian Foundation for Fundamental Research, Rae Bareli, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Babban Jee
- Department of Health Research, Ministry of Health and Family Welfare Government of India, New Delhi, India
| | - Nikolay Yu Gorobets
- Department of Organic and Bioorganic Chemistry, State Scientific Institution 'Institute for Single Crystals' of National Academy of Science of Ukraine, Kharkiv, Ukraine
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida, India
| | - Mukesh Kumar
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, USA
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Peng Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, PR China
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Martin Zoltner
- Drug Discovery and Evaluation Unit, Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| |
Collapse
|
10
|
Natural Compounds as Non-Nucleoside Inhibitors of Zika Virus Polymerase through Integration of In Silico and In Vitro Approaches. Pharmaceuticals (Basel) 2022; 15:ph15121493. [PMID: 36558945 PMCID: PMC9788182 DOI: 10.3390/ph15121493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
Although the past epidemic of Zika virus (ZIKV) resulted in severe neurological consequences for infected infants and adults, there are still no approved drugs to treat ZIKV infection. In this study, we applied computational approaches to screen an in-house database of 77 natural and semi-synthetic compounds against ZIKV NS5 RNA-dependent RNA-polymerase (NS5 RdRp), an essential protein for viral RNA elongation during the replication process. For this purpose, we integrated computational approaches such as binding-site conservation, chemical space analysis and molecular docking. As a result, we prioritized nine virtual hits for experimental evaluation. Enzymatic assays confirmed that pedalitin and quercetin inhibited ZIKV NS5 RdRp with IC50 values of 4.1 and 0.5 µM, respectively. Moreover, pedalitin also displayed antiviral activity on ZIKV infection with an EC50 of 19.28 µM cell-based assays, with low toxicity in Vero cells (CC50 = 83.66 µM) and selectivity index of 4.34. These results demonstrate the potential of the natural compounds pedalitin and quercetin as candidates for structural optimization studies towards the discovery of new anti-ZIKV drug candidates.
Collapse
|
11
|
Kumar A, Kumar D, Jose J, Giri R, Mysorekar IU. Drugs to limit Zika virus infection and implication for maternal-fetal health. FRONTIERS IN VIROLOGY 2022; 2. [PMID: 37064602 PMCID: PMC10104533 DOI: 10.3389/fviro.2022.928599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although the placenta has robust defense mechanisms that protect the fetus from a viral infection, some viruses can manipulate or evade these mechanisms and disrupt physiology or cross the placental barrier. It is well established that the Zika virus is capable of vertical transmission from mother to fetus and can cause malformation of the fetal central nervous system (i.e., microcephaly), as well as Guillain-Barre syndrome in adults. This review seeks to gather and assess the contributions of translational research associated with Zika virus infection, including maternal-fetal vertical transmission of the virus. Nearly 200 inhibitors that have been evaluated in vivo and/or in vitro for their therapeutic properties against the Zika virus are summarized in this review. We also review the status of current vaccine candidates. Our main objective is to provide clinically relevant information that can guide future research directions and strategies for optimized treatment and preventive care of infections caused by Zika virus or similar pathogens.
Collapse
Affiliation(s)
- Ankur Kumar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO-Kamand, Mandi, India
| | - Deepak Kumar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, State College, United States
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO-Kamand, Mandi, India
| | - Indira U. Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- CORRESPONDENCE Indira U. Mysorekar,
| |
Collapse
|
12
|
Muddapur UM, Badiger S, Shaikh IA, Ghoneim MM, Alshamrani SA, Mahnashi MH, Alsaikhan F, El-Sherbiny M, Al-Serwi RH, Khan AAL, Mannasaheb BA, Bahafi A, Iqubal SS, Begum T, Gouse HSM, Mohammed T, Hombalimath VS. Molecular modelling and simulation techniques to investigate the effects of fungal metabolites on the SARS-CoV-2 RdRp protein inhibition. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:102147. [PMID: 35702575 PMCID: PMC9186507 DOI: 10.1016/j.jksus.2022.102147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022]
Abstract
Various protein/receptor targets have been discovered through in-silico research. They are expanding rapidly due to their extensive advantage of delivering new drug candidates more quickly, efficiently, and at a lower cost. The automation of organic synthesis and biochemical screening will lead to a revolution in the entire research arena in drug discovery. In this research article, a few fungal metabolites were examined through an in-silico approach which involves major steps such as (a) Molecular Docking Analysis, (b) Drug likeness and ADMET studies, and (c) Molecular Dynamics Simulation. Fungal metabolites were taken from Antibiotic Database which showed antiviral effects on severe viral diseases such as HIV. Docking, Lipinski's, and ADMET analyses investigated the binding affinity and toxicity of five metabolites: Chromophilone I, iso; F13459; Stachyflin, acetyl; A-108836; Integracide A (A-108835). Chromophilone I, iso was subjected to additional analysis, including a 50 ns MD simulation of the protein to assess the occurring alterations. This molecule's docking data shows that it had the highest binding affinity. ADMET research revealed that the ligand might be employed as an oral medication. MD simulation revealed that the ligand–protein interaction was stable. Finally, this ligand can be exploited to develop SARS-CoV-2 therapeutic options. Fungal metabolites that have been studied could be a potential source for future lead candidates. Further study of these molecules may result in creating an antiviral drug to battle the SARS-CoV-2 virus.
Collapse
|
13
|
Repurposing of the antihistamine mebhydrolin napadisylate for treatment of Zika virus infection. Bioorg Chem 2022; 128:106024. [PMID: 35901544 DOI: 10.1016/j.bioorg.2022.106024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/16/2022] [Accepted: 07/10/2022] [Indexed: 11/20/2022]
Abstract
Zika virus (ZIKV) infection can lead to severe neurological disorders and fetal defects, which has become a public health problem worldwide. However, effective clinical treatment for ZIKV infection was still arduous. Antihistamines are attractive candidates for drug repurposing due to their low price and widespread availability. Here we screened FDA-approved antihistamine drugs to obtain anti-ZIKV candidate compounds and identified mebhydrolin napadisylate (MHL) that exhibits the potent inhibition of ZIKV infection in various cell lines in a histamine H1 receptor-independent manner. Mechanistic studies suggest that MHL acts as a ZIKV NS5 RNA-dependent RNA polymerase (RdRp) inhibitor, supported by a structure-activity relationship (SAR) analysis showing the correlation between the inhibitory effect upon viral RNA synthesis and ZIKV infectivity. Furthermore, MHL was shown to bind ZIKV NS5 RdRp in vitro and predicted to interact with key residues at the active site of ZIKV NS5 RdRp by molecular docking analysis. Our data together suggest that MHL suppresses ZIKV infection through the inhibition of ZIKV NS5 RdRp activity. This study highlights that MHL might be a promising clinical anti-ZIKV therapeutic.
Collapse
|
14
|
Alamri MA, Mirza MU, Adeel MM, Ashfaq UA, Tahir ul Qamar M, Shahid F, Ahmad S, Alatawi EA, Albalawi GM, Allemailem KS, Almatroudi A. Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors. Pharmaceuticals (Basel) 2022; 15:ph15060659. [PMID: 35745579 PMCID: PMC9228520 DOI: 10.3390/ph15060659] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/17/2022] Open
Abstract
Rift valley fever virus (RVFV) is the causative agent of a viral zoonosis that causes a significant clinical burden in domestic and wild ruminants. Major outbreaks of the virus occur in livestock, and contaminated animal products or arthropod vectors can transmit the virus to humans. The viral RNA-dependent RNA polymerase (RdRp; L protein) of the RVFV is responsible for viral replication and is thus an appealing drug target because no effective and specific vaccine against this virus is available. The current study reported the structural elucidation of the RVFV-L protein by in-depth homology modeling since no crystal structure is available yet. The inhibitory binding modes of known potent L protein inhibitors were analyzed. Based on the results, further molecular docking-based virtual screening of Selleckchem Nucleoside Analogue Library (156 compounds) was performed to find potential new inhibitors against the RVFV L protein. ADME (Absorption, Distribution, Metabolism, and Excretion) and toxicity analysis of these compounds was also performed. Besides, the binding mechanism and stability of identified compounds were confirmed by a 50 ns molecular dynamic (MD) simulation followed by MM/PBSA binding free energy calculations. Homology modeling determined a stable multi-domain structure of L protein. An analysis of known L protein inhibitors, including Monensin, Mycophenolic acid, and Ribavirin, provide insights into the binding mechanism and reveals key residues of the L protein binding pocket. The screening results revealed that the top three compounds, A-317491, Khasianine, and VER155008, exhibited a high affinity at the L protein binding pocket. ADME analysis revealed good pharmacodynamics and pharmacokinetic profiles of these compounds. Furthermore, MD simulation and binding free energy analysis endorsed the binding stability of potential compounds with L protein. In a nutshell, the present study determined potential compounds that may aid in the rational design of novel inhibitors of the RVFV L protein as anti-RVFV drugs.
Collapse
Affiliation(s)
- Mubarak A. Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 16273, Saudi Arabia;
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada;
| | - Muhammad Muzammal Adeel
- 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China;
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
- Correspondence: (M.T.u.Q.); (K.S.A.)
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (U.A.A.); (F.S.)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - Eid A. Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Ghadah M. Albalawi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
- Department of Laboratory and Blood Bank, King Fahd Specialist Hospital, Tabuk 47717, Saudi Arabia
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
- Correspondence: (M.T.u.Q.); (K.S.A.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (G.M.A.); (A.A.)
| |
Collapse
|
15
|
Chalcones from Angelica keiskei (ashitaba) inhibit key Zika virus replication proteins. Bioorg Chem 2022; 120:105649. [PMID: 35124513 PMCID: PMC9187613 DOI: 10.1016/j.bioorg.2022.105649] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/25/2022]
Abstract
Zika virus (ZIKV) is a dangerous human pathogen and no antiviral drugs have been approved to date. The chalcones are a group of small molecules that are found in a number of different plants, including Angelica keiskei Koidzumi, also known as ashitaba. To examine chalcone anti-ZIKV activity, three chalcones, 4-hydroxyderricin (4HD), xanthoangelol (XA), and xanthoangelol-E (XA-E), were purified from a methanol-ethyl acetate extract from A. keiskei. Molecular and ensemble docking predicted that these chalcones would establish multiple interactions with residues in the catalytic and allosteric sites of ZIKV NS2B-NS3 protease, and in the allosteric site of the NS5 RNA-dependent RNA-polymerase (RdRp). Machine learning models also predicted 4HD, XA and XA-E as potential anti-ZIKV inhibitors. Enzymatic and kinetic assays confirmed chalcone inhibition of the ZIKV NS2B-NS3 protease allosteric site with IC50s from 18 to 50 µM. Activity assays also revealed that XA, but not 4HD or XA-E, inhibited the allosteric site of the RdRp, with an IC50 of 6.9 µM. Finally, we tested these chalcones for their anti-viral activity in vitro with Vero cells. 4HD and XA-E displayed anti-ZIKV activity with EC50 values of 6.6 and 22.0 µM, respectively, while XA displayed relatively weak anti-ZIKV activity with whole cells. With their simple structures and relative ease of modification, the chalcones represent attractive candidates for hit-to-lead optimization in the search of new anti-ZIKV therapeutics.
Collapse
|
16
|
Differential detection of zika virus based on PCR. J Virol Methods 2022; 301:114459. [PMID: 35007627 DOI: 10.1016/j.jviromet.2022.114459] [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: 07/28/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022]
Abstract
Tropical countries are highly prone to infectious diseases such as the one caused by zika virus. Infection by zika is clinically and epidemiologically highly relevant. For example, when women are infected by zika during the first trimester of pregnancy, the child incurs a high risk of microcephaly and acute neurological syndromes. In adults, the virus is associated with the Guillain-Barré syndrome and other disorders. The worldwide emergency caused by zika in 2013/14 demonstrated the need for rapid and accurate diagnostic tools for the virus. Current diagnostic methods include virus isolation, serological tests, and molecular assays. However, virus isolation requires labor-intensive and time-consuming cell culture; serological detection suffers from cross-reactivity caused by previous exposure to homologous arboviruses that cause symptoms like those caused by zika, while molecular tools commonly are not designed for differential zika detection. This work reports on developing a specific molecular detection method based on phylogenetically conserved primers designed for the specific diagnosis of the zika virus. The zika primers were systematically selected through a rigorous bioinformatic analysis and demonstrated the capability to be highly specific. We tested our primers on synthetic DNA, cell cultures and samples from patients infected with zika, dengue and chikungunya and found that they detected zika with specificity high enough for differential virus diagnosis.
Collapse
|
17
|
Chikungunya nsP4 homology modeling reveals a common motif with Zika and Dengue RNA polymerases as a potential therapeutic target. J Mol Model 2021; 27:247. [PMID: 34386905 DOI: 10.1007/s00894-021-04868-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Among the diseases transmitted by vectors, there are those caused by viruses named arboviruses (arthropod-borne viruses). In past years, viruses transmitted by mosquitoes have been of relevance in global health, such as Chikungunya (CHIKV), Dengue (DENV), and Zika (ZIKV), which have Aedes aegypti as a common vector, thus raising the possibility of multi-infection. Previous reports have described the general structure of RNA-dependent RNA polymerases termed right-hand fold, which is conserved in positive single-stranded RNA viruses. Here, we report a comparison between sequences and the computational structure of RNA-dependent RNA polymerases from CHIKV, DENV, and ZIKV and the conserved sites to be considered for the design of an antiviral drug against the three viruses. We show that the sequential identity between consensus sequences from CHIKV and DENV is 8.1% and the similarity is 15.1%; the identity between CHIKV and ZIKV is 9.3%, and the similarity is 16.6%; and the identity between DENV and ZIKV is 68.6%, and the similarity is 79.2%. Nevertheless, the structural alignment shows that the root-mean-square deviation (RMSD) measurement value in general structure comparison between CHIKV RdRp and ZIKV RdRp was 1.248 Å, RMSD between CHIKV RdRp and DENV RdRp was 1.070 Å, and RMSD between ZIKV RdRp and DENV RdRp was 1.106 Å. Despite the low identity and similarity of CHIKV sequence with DENV and ZIKV, we show that A, B, C, and E motifs are structurally well conserved. These structural similarities offer a window into drug design against these arboviruses giving clues about critical target sites.
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
Loaiza-Cano V, Monsalve-Escudero LM, Restrepo MP, Quintero-Gil DC, Pulido Muñoz SA, Galeano E, Zapata W, Martinez-Gutierrez M. In Vitro and In Silico Anti-Arboviral Activities of Dihalogenated Phenolic Derivates of L-Tyrosine. Molecules 2021; 26:3430. [PMID: 34198817 PMCID: PMC8201234 DOI: 10.3390/molecules26113430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022] Open
Abstract
Despite the serious public health problem represented by the diseases caused by dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) viruses, there are still no specific licensed antivirals available for their treatment. Here, we examined the potential anti-arbovirus activity of ten di-halogenated compounds derived from L-tyrosine with modifications in amine and carboxyl groups. The activity of compounds on VERO cell line infection and the possible mechanism of action of the most promising compounds were evaluated. Finally, molecular docking between the compounds and viral and cellular proteins was evaluated in silico with Autodock Vina®, and the molecular dynamic with Gromacs®. Only two compounds (TDC-2M-ME and TDB-2M-ME) inhibited both ZIKV and CHIKV. Within the possible mechanism, in CHIKV, the two compounds decreased the number of genome copies and in the pre-treatment strategy the infectious viral particles. In the ZIKV model, only TDB-2M-ME inhibited the viral protein and demonstrate a virucidal effect. Moreover, in the U937 cell line infected with CHIKV, both compounds inhibited the viral protein and TDB-2M-ME inhibited the viral genome too. Finally, the in silico results showed a favorable binding energy between the compounds and the helicases of both viral models, the NSP3 of CHIKV and cellular proteins DDC and β2 adrenoreceptor.
Collapse
Affiliation(s)
- Vanessa Loaiza-Cano
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
| | - Laura Milena Monsalve-Escudero
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
| | - Manuel Pastrana Restrepo
- Grupo de Investigación en Productos Naturales Marinos, Universidad de Antioquia, Medellín 050001, Colombia; (M.P.R.); (E.G.)
| | - Diana Carolina Quintero-Gil
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
| | | | - Elkin Galeano
- Grupo de Investigación en Productos Naturales Marinos, Universidad de Antioquia, Medellín 050001, Colombia; (M.P.R.); (E.G.)
| | - Wildeman Zapata
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050001, Colombia;
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680005, Colombia; (V.L.-C.); (L.M.M.-E.); (D.C.Q.-G.)
| |
Collapse
|
20
|
Virtual Screening and Molecular Docking Studies for Discovery of Potential RNA-Dependent RNA Polymerase Inhibitors. CRYSTALS 2021. [DOI: 10.3390/cryst11050471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The current COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Globally, this pandemic has affected over 111 million individuals and posed many health and economic challenges. Much research effort is dedicated to discovering new treatments to address the associated challenges and restrict the spread of SARS-CoV-2. Since SARS-CoV-2 is a positive-strand RNA virus, its replication requires the viral RNA-dependent RNA polymerase (RdRp) enzyme. In this study, we report the discovery of new potential RdRp enzyme inhibitors based on computer modeling and simulation methodologies. The antiviral ZINC database was utilized for covalent docking virtual screening followed by molecular inter-action analyses based on reported hot spots within the RdRp binding pocket (PDB: 7BV2). Eleven molecules, ZINC000014944915, ZINC000027556215, ZINC000013556344, ZINC000003589958, ZINC000003833965, ZINC000001642252, ZINC000028525778, ZINC000027557701, ZINC000013781295, ZINC000001651128 and ZINC000013473324, were shown to have the highest binding interactions. These molecules were further assessed by molecular dynamics (MD) simu-lations and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies. The results showed that all 11 molecules except ZINC000027557701 formed stable complexes with the viral RdRp and fell within the accepted ADMET parameters. The identified molecules can be used to design future potential RdRp inhibitors.
Collapse
|
21
|
Fernandes RS, de Godoy AS, Santos IA, Noske GD, de Oliveira KIZ, Gawriljuk VO, Gomes Jardim AC, Oliva G. Discovery of an imidazonaphthyridine and a riminophenazine as potent anti-Zika virus agents through a replicon-based high-throughput screening. Virus Res 2021; 299:198388. [PMID: 33887282 DOI: 10.1016/j.virusres.2021.198388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/19/2021] [Accepted: 03/06/2021] [Indexed: 12/17/2022]
Abstract
The 2015/16 Zika virus (ZIKV) epidemic led to almost 1 million confirmed cases in 84 countries and was associated to the development of congenital microcephaly and Guillain-Barré syndrome. More recently, a ZIKV African lineage was identified in Brazil raising concerns about a future outbreak. The long-term consequences of viral infection emphasizes the need for the development of effective anti-ZIKV drugs. In this study, we developed and characterized a ZIKV replicon cell line for the screening of viral replication inhibitors. The replicon system was developed by engineering the IRES-Neo cassette into the 3' UTR terminus of the ZIKV Rluc DNA construct. After in vitro transcription, replicon RNA was used to transfect BHK-21 cells, that were selected with G418, thus generating the BHK-21-RepZIKV_IRES-Neo cell line. Through this replicon-based cell system, we identified two molecules with potent anti-ZIKV activities, an imidazonaphthyridine and a riminophenazine, both from the MMV/DNDi Pandemic Response Box library of 400 drug-like compounds. The imidazonaphthyridine, known as RO8191, showed remarkable selectivity against ZIKV, while the riminophenazine, the antibiotic Clofazimine, could act as a non-nucleoside analog inhibitor of viral RNA-dependent RNA polymerase (RdRp), as evidenced both in vitro and in silico. The data showed herein supports the use of replicon-based assays in high-throughput screening format as a biosafe and reliable tool for antiviral drug discovery.
Collapse
Affiliation(s)
- Rafaela Sachetto Fernandes
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil.
| | - Andre Schutzer de Godoy
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Igor Andrade Santos
- Institute of Biomedical Sciences, Federal University of Uberlândia, Av. Amazonas, 1700, bloco 4C sala 216, Umuarama, Uberlândia, 38405-317, Brazil
| | - Gabriela Dias Noske
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Ketllyn Irene Zagato de Oliveira
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Victor Oliveira Gawriljuk
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Sciences, Federal University of Uberlândia, Av. Amazonas, 1700, bloco 4C sala 216, Umuarama, Uberlândia, 38405-317, Brazil
| | - Glaucius Oliva
- Physics Institute of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| |
Collapse
|
22
|
Song W, Zhang H, Zhang Y, Chen Y, Lin Y, Han Y, Jiang J. Identification and Characterization of Zika Virus NS5 Methyltransferase Inhibitors. Front Cell Infect Microbiol 2021; 11:665379. [PMID: 33898335 PMCID: PMC8058401 DOI: 10.3389/fcimb.2021.665379] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/19/2021] [Indexed: 01/19/2023] Open
Abstract
The recurring outbreak of Zika virus (ZIKV) worldwide makes an emergent demand for novel, safe and efficacious anti-ZIKV agents. ZIKV non-structural protein 5 (NS5) methyltransferase (MTase), which is essential for viral replication, is regarded as a potential drug target. In our study, a luminescence-based methyltransferase assay was used to establish the ZIKV NS5 MTase inhibitor screening model. Through screening a natural product library, we found theaflavin, a polyphenol derived from tea, could inhibit ZIKV NS5 MTase activity with a 50% inhibitory concentration (IC50) of 10.10 μM. Molecular docking and site-directed mutagenesis analyses identified D146 as the key amino acid in the interaction between ZIKV NS5 MTase and theaflavin. The SPR assay indicated that theaflavin had a stronger binding activity with ZIKV NS5 wild-type (WT)-MTase than it with D146A-MTase. Moreover, theaflavin exhibited a dose dependent inhibitory effect on ZIKV replication with a 50% effective concentration (EC50) of 8.19 μM. All these results indicate that theaflavin is likely to be a promising lead compound against ZIKV.
Collapse
Affiliation(s)
- Weibao Song
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongjuan Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Chen
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanxing Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiandong Jiang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
23
|
Buendia-Atencio C, Pieffet GP, Montoya-Vargas S, Martínez Bernal JA, Rangel HR, Muñoz AL, Losada-Barragán M, Segura NA, Torres OA, Bello F, Suárez A, Rodríguez AK. Inverse Molecular Docking Study of NS3-Helicase and NS5-RNA Polymerase of Zika Virus as Possible Therapeutic Targets of Ligands Derived from Marcetia taxifolia and Its Implications to Dengue Virus. ACS OMEGA 2021; 6:6134-6143. [PMID: 33718704 PMCID: PMC7948243 DOI: 10.1021/acsomega.0c04719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/29/2021] [Indexed: 06/01/2023]
Abstract
Dengue and Zika are two mosquito-borne diseases of great impact on public health around the world in tropical and subtropical countries. DENV and ZIKV belong to the Flaviviridae family and the Flavivirus genus. Currently, there are no effective therapeutic agents to treat or prevent these pathologies. The main objective of this work was to evaluate potential inhibitors from active compounds obtained from Marcetia taxifolia by performing inverse molecular docking on ZIKV-NS3-helicase and ZIKV-NS5-RNA polymerase as targets. This computational strategy is based on renormalizing the binding scores of the compounds to these two proteins, allowing a direct comparison of the results across the proteins. The crystallographic structures of the ZIKV-NS3-helicase and ZIKV-NS5-RNA-polymerase proteins share a great similarity with DENV homologous proteins. The P-loop active site of the crystallographic structure of ZIKV-NS3-helicase presents a high percentage of homology with the four dengue serotypes. It was found that most ligands of the active compounds (5,3'-dihydroxy-3,6,7,8,4'-pentamethoxyflavone (5DP); 5-hydroxy-3,6,7,8,3',4'-hexamethoxyflavone (5HH); myricetin-3-O-rhamnoside (M3OR)) from Marcetia taxifolia had a better affinity for ZIKV-NS3-helicase than for ZIKV-NS5-RNA polymerase, as indicated by the negative multiple active site correction (MASC) score, except for M3RG that showed a higher affinity for ZIKV-NS5-RNA polymerase. On the other hand, the AutoDock Vina scores showed that M3OR had the highest score value (-9.60 kcal/mol) and the highest normalized score (1.13) against ZIKV-NS3-helicase. These results in silico demonstrated that the nonstructural proteins NS3-helicase and NS5-RNA polymerase, which share similar molecular structures between the selected viruses, could become therapeutic targets for some bioactive compounds derived from Marcetia taxifolia.
Collapse
Affiliation(s)
| | - Gilles Paul Pieffet
- Faculty
of Science, Universidad Antonio Nariño
(UAN), Bogotá 110231, Colombia
| | | | | | - Héctor Rafael Rangel
- Laboratory
of Molecular Virology, Instituto Venezolano
de Investigaciones Científicas, Caracas 1204, Venezuela
| | - Ana Luisa Muñoz
- PhD
Program of Health Science, Universidad Antonio
Nariño (UAN), Bogotá 110231, Colombia
| | | | - Nidya Alexandra Segura
- Faculty
of Science, Universidad Pedagógica
y Tecnológica de Colombia, Tunja150003, Colombia
| | - Orlando A. Torres
- Faculty
of
Veterinary Medicine, Universidad Antonio
Nariño (UAN), Bogotá 110231, Colombia
| | - Felio Bello
- Faculty
of Agricultural and Livestock Sciences, Program of Veterinary Medicine, Universidad de La Salle, Bogotá 110131 Colombia
| | - Alírica
Isabel Suárez
- Natural
Products Laboratory, Faculty of Pharmacy, Universidad Central de Venezuela, Caracas 1050, Venezuela
| | | |
Collapse
|
24
|
Kumar S, Sharma PP, Upadhyay C, Kempaiah P, Rathi B, Poonam. Multi-targeting approach for nsp3, nsp9, nsp12 and nsp15 proteins of SARS-CoV-2 by Diosmin as illustrated by molecular docking and molecular dynamics simulation methodologies. Methods 2021; 195:44-56. [PMID: 33639316 PMCID: PMC7904494 DOI: 10.1016/j.ymeth.2021.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/01/2022] Open
Abstract
Novel coronavirus SARS-CoV-2continues tospread rapidly worldwide and causing serious health and economic loss. In the absence of any effective treatment, various in-silico approaches are being explored towards the therapeutic discovery against COVID-19. Targeting multiple key enzymes of SARS-CoV-2 with a single potential drug could be an important in-silico strategy to tackle the therapeutic emergency. A number of Food and Drug Administration (FDA) approved drugs entered into clinical stages were originated from multi-target approaches with an increased rate, 16-21% between 2015 and 2017. In this study, we selected an FDA-approved library (Prestwick Chemical Library of 1520 compounds) and implemented in-silico virtual screening against multiple protein targets of SARS-CoV-2 on the Glide module of Schrödinger software (release 2020-1). Compounds were analyzed for their docking scores and the top-ranked against each targeted protein were further subjected to Molecular Dynamics (MD) simulations to assess the binding stability of ligand-protein complexes. A multi-targeting approach was optimized that enabled the analysis of several compounds' binding efficiency with more than one protein targets. It was demonstrated that Diosmin (6) showed the highest binding affinity towards multiple targets with binding free energy (kcal/mol) values of -63.39 (nsp3); -62.89 (nsp9); -31.23 (nsp12); and -65.58 (nsp15). Therefore, our results suggests that Diosmin (6) possesses multi-targeting capability, a potent inhibitor of various non-structural proteins of SARS-CoV-2, and thus it deserves further validation experiments before using as a therapeutic against COVID-19 disease.
Collapse
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi 110007, India
| | - Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Hansraj College, University of Delhi, Delhi 110007, India
| | - Charu Upadhyay
- Department of Chemistry, Miranda House, University of Delhi, Delhi 110007, India
| | - Prakasha Kempaiah
- Department of Medicine, Loyola University Stritch School of Medicine, Chicago, IL 60153, United States
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Hansraj College, University of Delhi, Delhi 110007, India
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi 110007, India.
| |
Collapse
|
25
|
Morris G, Bortolasci CC, Puri BK, Olive L, Marx W, O'Neil A, Athan E, Carvalho A, Maes M, Walder K, Berk M. Preventing the development of severe COVID-19 by modifying immunothrombosis. Life Sci 2021; 264:118617. [PMID: 33096114 PMCID: PMC7574725 DOI: 10.1016/j.lfs.2020.118617] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND COVID-19-associated acute respiratory distress syndrome (ARDS) is associated with significant morbidity and high levels of mortality. This paper describes the processes involved in the pathophysiology of COVID-19 from the initial infection and subsequent destruction of type II alveolar epithelial cells by SARS-CoV-2 and culminating in the development of ARDS. MAIN BODY The activation of alveolar cells and alveolar macrophages leads to the release of large quantities of proinflammatory cytokines and chemokines and their translocation into the pulmonary vasculature. The presence of these inflammatory mediators in the vascular compartment leads to the activation of vascular endothelial cells platelets and neutrophils and the subsequent formation of platelet neutrophil complexes. These complexes in concert with activated endothelial cells interact to create a state of immunothrombosis. The consequence of immunothrombosis include hypercoagulation, accelerating inflammation, fibrin deposition, migration of neutrophil extracellular traps (NETs) producing neutrophils into the alveolar apace, activation of the NLRP3 inflammazome, increased alveolar macrophage destruction and massive tissue damage by pyroptosis and necroptosis Therapeutic combinations aimed at ameliorating immunothrombosis and preventing the development of severe COVID-19 are discussed in detail.
Collapse
Affiliation(s)
- Gerwyn Morris
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Chiara C Bortolasci
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; Deakin University, Centre for Molecular and Medical Research, School of Medicine, Geelong, Australia
| | | | - Lisa Olive
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; School of Psychology, Deakin University, Geelong, Australia
| | - Wolfgang Marx
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia
| | - Adrienne O'Neil
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; Melbourne School of Population and Global Health, Melbourne, Australia
| | - Eugene Athan
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; Barwon Health, Geelong, Australia
| | - Andre Carvalho
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; Department of Psychiatry, University of Toronto, Toronto, Canada; Centre for Addiction and Mental Health (CAMH), Toronto, Canada
| | - Michael Maes
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; Department of Psychiatry, King Chulalongkorn University Hospital, Bangkok, Thailand; Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Ken Walder
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; Deakin University, Centre for Molecular and Medical Research, School of Medicine, Geelong, Australia
| | - Michael Berk
- Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia; Orygen, The National Centre of Excellence in Youth Mental Health, Centre for Youth Mental Health, Florey Institute for Neuroscience and Mental Health and the Department of Psychiatry, The University of Melbourne, Melbourne, Australia.
| |
Collapse
|
26
|
Baltina LA, Hour MJ, Liu YC, Chang YS, Huang SH, Lai HC, Kondratenko RM, Petrova SF, Yunusov MS, Lin CW. Antiviral activity of glycyrrhizic acid conjugates with amino acid esters against Zika virus. Virus Res 2020; 294:198290. [PMID: 33388394 DOI: 10.1016/j.virusres.2020.198290] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 12/15/2020] [Accepted: 12/25/2020] [Indexed: 12/24/2022]
Abstract
Zika virus (ZIKV) is a new pathogenic flavivirus transmitted by mosquitoes Aedes spp. ZIKV infection is accompanied by serious neurological complications and is especially dangerous for pregnant women, in which it can lead to congenital malformations of the fetus and microcephaly in neonates. Currently, there are no licensed vaccines or specific post-infectious therapies for ZIKV infection. This report is devoted to the study of glycyrrhizic acid (GL) derivatives as ZIKV inhibitors. The inhibitory assays on the cytopathic effect (CPE) and viral infectivity of ZIKV in three different human cell lines revealed that the conjugation of GL with amino acids and their esters (methyl, ethyl) is influenced by the antiviral activity of the compounds. GL conjugates with Glu(OMe)-OMe 11, Glu(OH)-OMe 12, Asp(OMe)-OMe 13, TyrOMe 14, LeuOEt 15, and PheOEt 16 with free COOH groups in the triterpene moiety were active against ZIKV. The most active compounds 13 and 14 have IC50 values of 0.23 μM and 0.09 μM against low doses (MOI = 0.05) of ZIKV strain PRVABC59, 1.20 μM and 0.74 μM against high doses (MOI = 10) of ZIKV strain Natal RGN single-round infectious particles, respectively. The lead compound was 14 with a high selectivity index (SI < 500). Compound 13 showed a higher inhibitory effect on the early stage (entry) of ZIKV replication than compound 14, and was less potent than compound 14 at the post-entry stage, consistent with the docking models. Compounds 13 and 14 also had a strong interaction with the active site pocket of NS5 MTase. Compounds 13 and 14 are recommended for expanded antiviral studies against ZIKV infection.
Collapse
Affiliation(s)
- Lidia A Baltina
- Ufa Institute of Chemistry, Ufa Federal Research Centre of RAS, Ufa, 450054, Russian Federation.
| | - Mann-Jen Hour
- School of Pharmacy, China Medical University, Taichung, 40402, Taiwan
| | - Ya-Chi Liu
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 40402, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Young-Sheng Chang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 40402, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Su-Hua Huang
- Department of Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Hsueh-Chou Lai
- Division of Hepato-gastroenterology, Department of Internal Medicine, China Medical University Hospital, Taichung, 40447, Taiwan
| | | | - Svetlana F Petrova
- Ufa Institute of Chemistry, Ufa Federal Research Centre of RAS, Ufa, 450054, Russian Federation
| | - Marat S Yunusov
- Ufa Institute of Chemistry, Ufa Federal Research Centre of RAS, Ufa, 450054, Russian Federation
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 40402, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, 40402, Taiwan; Department of Biotechnology, Asia University, Taichung 41354, Taiwan.
| |
Collapse
|
27
|
Noreen, Ali R, Badshah SL, Faheem M, Abbasi SW, Ullah R, Bari A, Jamal SB, Mahmood HM, Haider A, Haider S. Identification of potential inhibitors of Zika virus NS5 RNA-dependent RNA polymerase through virtual screening and molecular dynamic simulations. Saudi Pharm J 2020; 28:1580-1591. [PMID: 33424251 PMCID: PMC7783101 DOI: 10.1016/j.jsps.2020.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
Zika virus (ZIKV) is one of the mosquito borne flavivirus with several outbreaks in past few years in tropical and subtropical regions. The non-structural proteins of flaviviruses are suitable active targets for inhibitory drugs due to their role in pathogenicity. In ZIKV, the non-structural protein 5 (NS5) RNA-Dependent RNA polymerase replicates its genome. Here we have performed virtual screening to identify suitable ligands that can potentially halt the ZIKV NS5 RNA dependent RNA polymerase (RdRp). During this process, we searched and screened a library of ligands against ZIKV NS5 RdRp. The selected ligands with significant binding energy and ligand-receptor interactions were further processed. Among the selected docked conformations, top five was further optimized at atomic level using molecular dynamic simulations followed by binding free energy calculations. The interactions of ligands with the target structure of ZIKV RdRp revealed that they form strong bonds within the active sites of the receptor molecule. The efficacy of these drugs against ZIKV can be further analyzed through in-vitro and in-vivo studies.
Collapse
Affiliation(s)
- Noreen
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Roshan Ali
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmacuitcal Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Hafiz Majid Mahmood
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Adnan Haider
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sajjad Haider
- Department of Chemical Engineering, College of Engineering, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
28
|
Non-nucleoside Inhibitors of Zika Virus RNA-Dependent RNA Polymerase. J Virol 2020; 94:JVI.00794-20. [PMID: 32796069 DOI: 10.1128/jvi.00794-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/02/2020] [Indexed: 02/08/2023] Open
Abstract
Zika virus (ZIKV) remains a potentially significant public health concern because it can cause teratogenic effects, such as microcephaly in newborns and neurological disease, like Guillain-Barré syndrome. Together with efforts to develop a vaccine, the discovery of antiviral molecules is important to control ZIKV infections and to prevent its most severe symptoms. Here, we report the development of small nonnucleoside inhibitors (NNIs) of ZIKV RNA-dependent RNA polymerase (RdRp) activity. These NNIs target an allosteric pocket (N pocket) located next to a putative hinge region between the thumb and the palm subdomains that was originally described for dengue virus (DENV) RdRp. We first tested the activity of DENV RdRp N-pocket inhibitors against ZIKV RdRp, introduced chemical modifications into these molecules, and assessed their potency using both enzymatic and cell-based assays. The most potent compound had a 50% inhibitory concentration value of 7.3 μM and inhibited ZIKV replication in a cell-based assay with a 50% effective concentration value of 24.3 μM. Importantly, we report four high-resolution crystal structures detailing how these NNIs insert into the N pocket of ZIKV RdRp. Our observations point to subtle differences in the size, shape, chemical environment, and hydration of the N pocket from ZIKV RdRp from those of the N pocket from DENV RdRp that are crucial for the design of improved antiviral inhibitors with activity against ZIKV.IMPORTANCE Zika virus belongs to the Flavivirus genus, which comprises several important human pathogens. There is currently neither an approved vaccine nor antiviral drugs available to prevent infection by ZIKV. The nonstructural protein 5 (NS5) polymerase, which is responsible for replicating the viral RNA genome, represents one of the most promising targets for antiviral drug development. Starting from compounds recently developed against dengue virus NS5, we designed and synthesized inhibitors targeting Zika virus NS5. We show that these novel compounds inhibit viral replication by targeting the polymerase activity. High-resolution X-ray crystallographic structures of protein-inhibitor complexes demonstrated specific binding to an allosteric site within the polymerase, called the N pocket. This work paves the way for the future structure-based design of potent compounds specifically targeting ZIKV RNA polymerase activity.
Collapse
|
29
|
Jiang Y, Yin W, Xu HE. RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19. Biochem Biophys Res Commun 2020; 538:47-53. [PMID: 32943188 PMCID: PMC7473028 DOI: 10.1016/j.bbrc.2020.08.116] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global pandemic. Although great efforts have been made to develop effective therapeutic interventions, only the nucleotide analog remdesivir was approved for emergency use against COVID-19. Remdesivir targets the RNA-dependent RNA polymerase (RdRp), an essential enzyme for viral RNA replication and a promising drug target for COVID-19. Recently, several structures of RdRp in complex with substrate RNA and remdesivir were reported, providing insights into the mechanisms of RNA recognition by RdRp. These structures also reveal the mechanism of RdRp inhibition by nucleotide inhibitors and offer a molecular template for the development of RdRp-targeting drugs. This review discusses the recognition mechanism of RNA and nucleotide inhibitor by RdRp, and its implication in drug discovery.
Collapse
Affiliation(s)
- Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Wanchao Yin
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
30
|
Tunghirun C, Narkthong V, Chaicumpa W, Chimnaronk S. Interference of dengue replication by blocking the access of 3' SL RNA to the viral RNA-dependent RNA polymerase. Antiviral Res 2020; 182:104921. [PMID: 32835694 DOI: 10.1016/j.antiviral.2020.104921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/25/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023]
Abstract
The four circulating serotypes of dengue virus (DENV) occasionally cause potentially fetal symptoms of severe dengue, which there is currently no specific treatment available. Extensive efforts have been made to inhibit viral replication processes by impeding the activity of an exclusive RNA-dependent RNA polymerase (RdRp) in the viral non-structural protein 5 (NS5). In our earlier work, we identified the characteristic, specific interaction between the C-terminal thumb subdomain of RdRp and an apical loop in the 3' stem-loop (SL) element in the DENV RNA genome, which is fundamental for viral replication. Here, we demonstrated a new approach for interfering viral replication via blocking of 3' SL RNA binding to RdRp by the single-chain variable fragments (scFvs). We isolated and cloned 3 different human scFvs that bound to RdRp from DENV serotype 2 and interfered with 3' SL-binding, utilizing a combination of phage-display panning and Alpha methods. When tagged with a cell penetrating peptide, a selected scFv clone, 2E3, entered cells and partially colocalized with NS5 in the cytoplasm of infected HuH-7 cells. 2E3 significantly inhibited DENV RNA replication with sub-nanomolar EC50 values and significantly reduced the production of infectious particles. The molecular docking models suggested that 2E3 recognized both palm and thumb subdomains of RdRp, and interacted with Lys841, a key residue involved in RNA binding. Our results provide a new potential therapeutic molecule specific for flaviviral infection.
Collapse
Affiliation(s)
- Chairat Tunghirun
- The Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand
| | - Veerakorn Narkthong
- Siriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sarin Chimnaronk
- The Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand; Siriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| |
Collapse
|
31
|
Ezzemani W, Windisch MP, Kettani A, Altawalah H, Nourlil J, Benjelloun S, Ezzikouri S. Immuno-informatics-based identification of novel potential B cell and T cell epitopes to fight Zika virus infections. Infect Disord Drug Targets 2020; 21:572-581. [PMID: 32778040 DOI: 10.2174/1871526520666200810153657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/23/2020] [Accepted: 06/23/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Globally, the recent outbreak of Zika virus (ZIKV) in Brazil, Asia Pacific, and other countries highlighted the unmet medical needs. Currently, there are neither effective vaccines nor therapeutics available to prevent or treat ZIKV infection. OBJECTIVE In this study, we aimed to design an epitope-based vaccine for ZIKV using an in silico approach to predict and analyze B- and T-cell epitopes. METHODS The prediction of the most antigenic epitopes has targeted the capsid and the envelope proteins as well as nonstructural proteins NS5 and NS3 using immune-informatics tools PROTPARAM, CFSSP, PSIPRED, and Vaxijen v2.0. B and T-cell epitopes were predicted using ABCpred, IEDB, TepiTool, and their toxicity were evaluated using ToxinPred. The 3-dimensional epitope structures were generated by PEP-FOLD. Energy minimization was performed using Swiss-Pdb Viewer, and molecular docking was conducted using PatchDock and FireDock server. RESULTS As a result, we predicted 307 epitopes of MHCI (major histocompatibility complex class I) and 102 epitopes of MHCII (major histocompatibility complex class II). Based on immunogenicity and antigenicity scores, we identified the four most antigenic MHC I epitopes: MVLAILAFLR (HLA-A*68 :01), ETLHGTVTV (HLA-A*68 :02), DENHPYRTW (HLA-B*44 :02),QEGVFHTMW (HLA-B*44 :03) and TASGRVIEEW (HLA-B*58:01), and MHC II epitopes: IIKKFKKDLAAMLRI (HLA-DRB3*02 :02), ENSKMMLELDPPFGD (HLA-DRB3*01:01), HAETWFFDENHPYRT (HLA-DRB3*01:01), TDGVYRVMTRRLLGS (HLA-DRB1*11 :01), and DGCWYGMEIRPRKEP (HLA-DRB5*01:01). CONCLUSION This study provides novel potential B cell and T cell epitopes to fight Zika virus infections and may prompt further development of vaccines against ZIKV and other emerging infectious diseases. However, further investigations for protective immune response by in vitro and in vivo studies to ratify the immunogenicity, safety of the predicted structure, and ultimately the vaccine properties to prevent ZIKV infections are warranted.
Collapse
Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca. Morocco
| | - Marc P Windisch
- Applied Molecular Virology Laboratory, Discovery Biology Department, Institut Pasteur Korea, Seongnamsi, Gyeonggi-do. South Korea
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Département de Biologie, Faculté des Sciences Ben Msik, Hassan II University Of Casablanca. Morocco
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University. Kuwait
| | - Jalal Nourlil
- Medical Virology and BSL3 Laboratory, Institut Pasteur du Maroc, Casablanca. Morocco
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca. Morocco
| | - Sayeh Ezzikouri
- Laboratoire de Biologie et Santé (URAC34), Département de Biologie, Faculté des Sciences Ben Msik, Hassan II University Of Casablanca. Morocco
| |
Collapse
|
32
|
Wang B, Thurmond S, Zhou K, Sánchez-Aparicio MT, Fang J, Lu J, Gao L, Ren W, Cui Y, Veit EC, Hong H, Evans MJ, O'Leary SE, García-Sastre A, Zhou ZH, Hai R, Song J. Structural basis for STAT2 suppression by flavivirus NS5. Nat Struct Mol Biol 2020; 27:875-885. [PMID: 32778820 PMCID: PMC7554153 DOI: 10.1038/s41594-020-0472-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/25/2020] [Indexed: 11/23/2022]
Abstract
Suppressing cellular signal transducers of transcription 2 (STAT2) is a common strategy viruses use to establish infections, yet the detailed mechanism remains elusive due to lack of structural information of the viral-cellular complex involved. Here, we report the cryo-EM and crystal structures of human STAT2 (hSTAT2) in complex with the non-structural protein 5 (NS5) of Zika virus (ZIKV) and dengue virus (DENV), revealing two-pronged interactions between NS5 and hSTAT2. First, the NS5 methyltransferase and RNA-dependent RNA polymerase (RdRP) domains form a conserved inter-domain cleft harboring the coiled-coil domain of hSTAT2, thus preventing association of hSTAT2 with interferon regulatory factor 9. Second, the NS5 RdRP domain also binds the N-terminal domain of hSTAT2. Disruption of these ZIKV NS5–hSTAT2 interactions compromised NS5-mediated hSTAT2 degradation and interferon suppression, and viral infection under interferon-competent condition. Taken together, these results clarify the mechanism underlying the functional antagonism of STAT2 by both ZIKV and DENV.
Collapse
Affiliation(s)
- Boxiao Wang
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Stephanie Thurmond
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Cell, Molecular and Developmental Biology Graduate Program, University of California, Riverside, CA, USA
| | - Kang Zhou
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Maria T Sánchez-Aparicio
- GlobalHealth and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Linfeng Gao
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
| | - Wendan Ren
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Ethan C Veit
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - HeaJin Hong
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Matthew J Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seán E O'Leary
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Adolfo García-Sastre
- GlobalHealth and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, CA, USA. .,Departement of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA.
| | - Rong Hai
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA. .,Cell, Molecular and Developmental Biology Graduate Program, University of California, Riverside, CA, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, USA. .,Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA.
| |
Collapse
|
33
|
Antibiotic fidaxomicin is an RdRp inhibitor as a potential new therapeutic agent against Zika virus. BMC Med 2020; 18:204. [PMID: 32731873 PMCID: PMC7392643 DOI: 10.1186/s12916-020-01663-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/11/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Zika virus (ZIKV) infection is a global health problem, and its complications, including congenital Zika syndrome and Guillain-Barré syndrome, constitute a continued threat to humans. Unfortunately, effective therapeutics against ZIKV infection are not available thus far. METHODS We screened the compounds collection consisting of 1789 FDA-approved drugs by a computational docking method to obtain anti-ZIKV candidate compounds targeting ZIKV RNA-dependent RNA polymerase (RdRp). SPR (BIAcore) assay was employed to demonstrate the candidate compounds' direct binding to ZIKV RdRp, and polymerase activity assay was used to determine the inhibitory effect on ZIKV RdRp-catalyzed RNA synthesis. The antiviral effects on ZIKV in vitro and in vivo were detected in infected cultured cells and in Ifnar1-/- mice infected by ZIKV virus using plaque assay, western blotting, tissue immunofluorescence, and immunohistochemistry. RESULTS Here, we report that a first-in-class macrocyclic antibiotic, which has been clinically used to treat Clostridium difficile infection, fidaxomicin, potently inhibits ZIKV replication in vitro and in vivo. Our data showed that fidaxomicin was effective against African and Asian lineage ZIKV in a wide variety of cell lines of various tissue origins, and prominently suppressed ZIKV infection and significantly improved survival of infected mice. In addition, fidaxomicin treatment reduced the virus load in the brains and testes, and alleviated ZIKV-associated pathological damages, such as paralysis, hunching, and neuronal necrosis in the cerebra. Furthermore, our mechanistic study showed that fidaxomicin directly bound ZIKV NS5 protein and inhibited the RNA synthesis-catalyzing activity of ZIKV RdRp. CONCLUSIONS Our data suggest that fidaxomicin may represent an effective anti-ZIKV agent. In the light that fidaxomicin is already a clinically used drug, there might be a promising prospect in the development of fidaxomicin to be an antiviral therapeutic.
Collapse
|
34
|
Peng Q, Peng R, Yuan B, Zhao J, Wang M, Wang X, Wang Q, Sun Y, Fan Z, Qi J, Gao GF, Shi Y. Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2. Cell Rep 2020; 31:107774. [PMID: 32531208 PMCID: PMC7260489 DOI: 10.1016/j.celrep.2020.107774] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/23/2020] [Accepted: 05/26/2020] [Indexed: 01/18/2023] Open
Abstract
The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused a huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus (SARS-CoV-2). The viral polymerase is a promising antiviral target. Here, we describe the near-atomic-resolution structure of the SARS-CoV-2 polymerase complex consisting of the nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases and suggests a mechanism of activation by cofactors. Biochemical studies reveal reduced activity of the core polymerase complex and lower thermostability of individual subunits of SARS-CoV-2 compared with SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate adaptation of SARS-CoV-2 toward humans with a relatively lower body temperature than the natural bat hosts. Cryo-EM structure of SARS-CoV-2 nsp12-nsp7-nsp8 core polymerase complex The core complex of SARS-CoV-2 has lower enzymatic activity than SARS-CoV SARS-CoV-2 nsp7-8-12 subunits are less thermostable than the SARS-CoV counterpart
Collapse
Affiliation(s)
- Qi Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruchao Peng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Yuan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jingru Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xixi Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Sun
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing General Hospital, University of the Chinese Academy of Sciences, Chongqing 400013, China; College of Basic Medicine, Jilin University, Changchun, Jilin 130021, China.
| |
Collapse
|
35
|
Yun SI, Song BH, Woolley ME, Frank JC, Julander JG, Lee YM. Development, Characterization, and Application of Two Reporter-Expressing Recombinant Zika Viruses. Viruses 2020; 12:v12050572. [PMID: 32456014 PMCID: PMC7290298 DOI: 10.3390/v12050572] [Citation(s) in RCA: 4] [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: 05/03/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Zika virus (ZIKV), a mosquito-borne transplacentally transmissible flavivirus, is an enveloped virus with an ~10.8 kb plus-strand RNA genome that can cause neurological disease. To facilitate the identification of potential antivirals, we developed two reporter-expressing ZIKVs, each capable of expressing an enhanced green fluorescent protein or an improved luminescent NanoLuc luciferase. First, a full-length functional ZIKV cDNA clone was engineered as a bacterial artificial chromosome, with each reporter gene under the cap-independent translational control of a cardiovirus-derived internal ribosome entry site inserted downstream of the single open reading frame of the viral genome. Two reporter-expressing ZIKVs were then generated by transfection of ZIKV-susceptible BHK-21 cells with infectious RNAs derived by in vitro run-off transcription from the respective cDNAs. As compared to the parental virus, the two reporter-expressing ZIKVs grew to lower titers with slower growth kinetics and formed smaller foci; however, they displayed a genome-wide viral protein expression profile identical to that of the parental virus, except for two previously unrecognized larger forms of the C and NS1 proteins. We then used the NanoLuc-expressing ZIKV to assess the in vitro antiviral activity of three inhibitors (T-705, NITD-008, and ribavirin). Altogether, our reporter-expressing ZIKVs represent an excellent molecular tool for the discovery of novel antivirals.
Collapse
Affiliation(s)
- Sang-Im Yun
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Byung-Hak Song
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Michael E. Woolley
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Jordan C. Frank
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
| | - Justin G. Julander
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA; (S.-I.Y.); (B.-H.S.); (M.E.W.); (J.C.F.); (J.G.J.)
- Veterinary Diagnostics and Infectious Diseases, Utah Science Technology and Research, Utah State University, Logan, UT 84341, USA
- Correspondence: ; Tel.: +1-435-797-9667
| |
Collapse
|
36
|
Fajardo T, Sanford TJ, Mears HV, Jasper A, Storrie S, Mansur DS, Sweeney TR. The flavivirus polymerase NS5 regulates translation of viral genomic RNA. Nucleic Acids Res 2020; 48:5081-5093. [PMID: 32313955 PMCID: PMC7229856 DOI: 10.1093/nar/gkaa242] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 11/14/2022] Open
Abstract
Flaviviruses, including dengue virus and Zika virus, contain a single-stranded positive sense RNA genome that encodes viral proteins essential for replication and also serves as the template for new genome synthesis. As these processes move in opposite directions along the genome, translation must be inhibited at a defined point following infection to clear the template of ribosomes to allow efficient replication. Here, we demonstrate in vitro and in cell-based assays that the viral RNA polymerase, NS5, inhibits translation of the viral genome. By reconstituting translation in vitro using highly purified components, we show that this translation block occurs at the initiation stage and that translation inhibition depends on NS5-RNA interaction, primarily through association with the 5' replication promoter region. This work supports a model whereby expression of a viral protein signals successful translation of the infecting genome, prompting a switch to a ribosome depleted replication-competent form.
Collapse
Affiliation(s)
- Teodoro Fajardo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Thomas J Sanford
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Harriet V Mears
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Annika Jasper
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Skye Storrie
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Daniel S Mansur
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Trevor R Sweeney
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| |
Collapse
|
37
|
Bharadwaj S, Rao AK, Dwivedi VD, Mishra SK, Yadava U. Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation. J Biomol Struct Dyn 2020; 39:2338-2351. [PMID: 32216596 DOI: 10.1080/07391102.2020.1747545] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent Zika virus (ZIKV) outbreak and association with human diseases such as neurological disorders have raised global health concerns. However, in the absence of an approved anti-ZIKV drug has generated urgency for the drug development against ZIKV infection. Here, structure-based virtual screening of 8589 bioactive compounds, screened at the substrate-binding site of ZIKV nonstructural 5 (NS5)-based structure N-terminal methyltransferase (MTase) domain followed by ADMET (absorption, distribution, metabolism, excretion and toxicity) profiling concluded the four potential lead inhibitors, i.e. (4-acetylamino-benzenesulfonylamino)-acetic acid (F3342-0450), 3-(5-methylfuran-2-yl)-N-(4-sulfamoylphenyl)propanamide (F1736-0142), 8-(2-hydroxy-ethylamino)-1,3-dimethyl-7-(3-methyl-benzyl)-3,7-dihydro-purine-2,6-dione (F0886-0080) and N-[4-(aminosulfonyl)phenyl]-2,3-dihydro-1,4-benzodioxine-2-carboxamide (F0451-2187). Collectively, extra precision docking and Density Functional Theory(DFT) calculations studies identified the F3342-0450 molecule, having strong interactions on the active site of MTase, further supported by molecular dynamics simulation, binding affinity and hybrid QM/MM calculations, suggest a new drug molecule for the antiviral drug development against ZIKV infection. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shiv Bharadwaj
- Sabanci University Nanotechnology Research and Application Center, Istanbul, Turkey
| | - Akhilesh Kumar Rao
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| |
Collapse
|
38
|
Molecular dynamics simulation of zika virus NS5 RNA dependent RNA polymerase with selected novel non-nucleoside inhibitors. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127428] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
39
|
Kesari AS, Heintz VJ, Poudyal S, Miller AS, Kuhn RJ, LaCount DJ. Zika virus NS5 localizes at centrosomes during cell division. Virology 2020; 541:52-62. [PMID: 32056715 DOI: 10.1016/j.virol.2019.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/04/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) nonstructural protein 5 (NS5) plays a critical role in viral RNA replication and mediates key virus-host cell interactions. As with other flavivirus NS5 proteins, ZIKV NS5 is primarily found in the nucleus. We previously reported that the NS5 protein of dengue virus, another flavivirus, localized to centrosomes during cell division. Here we show that ZIKV NS5 also relocalizes from the nucleus to centrosomes during mitosis. In infected cells with supernumerary centrosomes, NS5 was present at all centrosomes. Transient expression of NS5 in uninfected cells confirmed that centrosomal localization was independent of other viral proteins. Live-cell imaging demonstrated that NS5-GFP accumulated at centrosomes shortly after break down of nuclear membrane and remained there through mitosis. Cells expressing NS5-GFP took longer to complete mitosis than control cells. Finally, an analysis of ZIKV NS5 binding partners revealed several centrosomal proteins, providing potential direct links between NS5 and centrosomes.
Collapse
Affiliation(s)
- Aditi S Kesari
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA; Department of Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Veronica J Heintz
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA; Department of Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Shishir Poudyal
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Andrew S Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Douglas J LaCount
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA; Department of Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
40
|
Ji W, Luo G. Zika virus NS5 nuclear accumulation is protective of protein degradation and is required for viral RNA replication. Virology 2020; 541:124-135. [DOI: 10.1016/j.virol.2019.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022]
|
41
|
Abstract
Zika virus (ZIKV) was once considered an obscure member of the large and diverse family of mosquito-borne flaviviruses, and human infections with ZIKV were thought to be sporadic, with mild and self-limiting symptoms. The large-scale ZIKV epidemics in the Americas and the unexpected uncovering of a link to congenital birth defects escalated ZIKV infections to the status of a global public health emergency. Recent studies that combined reverse genetics with modelling in multiple systems have provided evidence that ZIKV has acquired additional amino acid substitutions at the same time as congenital Zika syndrome and other birth defects were detected. In this Progress article, we summarize the evolution of ZIKV during its spread from Asia to the Americas and discuss potential links to pathogenesis.
Collapse
|
42
|
Elfiky AA. Novel guanosine derivatives against Zika virus polymerase in silico. J Med Virol 2020; 92:11-16. [PMID: 31436327 PMCID: PMC7166851 DOI: 10.1002/jmv.25573] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/17/2019] [Indexed: 01/06/2023]
Abstract
The Zika virus (ZIKV) outbreak, which started in the year 2015, is considered the fastest and most widely spread outbreak reported for this flavivirus. The polymerase domain of the NS5 protein has been targeted in other viral infections and is recognized as a suitable target in ZIKV infection. Different novel modified compounds against ZIKV NS5 have been tested in silico. A few structures have been solved for ZIKV polymerase and deposited in the protein data bank website. Two of these solved structures (with a resolution of less than 1.9 A) are used in this study to test the binding of 74 novel compounds in silico. Molecular docking is used to quantify the binding affinities of ZIKV polymerase and compare it to the hepatitis C virus NS5B. A total of 19 novel compounds revealed results that are either similar to or better than the physiological molecule, guanosine triphosphate. Water molecules are found to facilitate the binding of the compounds to ZIKV RNA-dependent RNA polymerase (RdRp) structures. The presented 19 novel compounds represent good binders to ZIKV RdRp and could be suitable candidates for developing a new and effective anti-ZIKV polymerase nucleotide inhibitor.
Collapse
Affiliation(s)
- Abdo A. Elfiky
- Biophysics Department, Faculty of SciencesCairo UniversityGizaEgypt
- Quantitative Life Science SectionThe Abdus Salam International Center for Theoretical Physics (ICTP), Strada CostieraTriesteItaly
| |
Collapse
|
43
|
Polymerase Activity, Protein-Protein Interaction, and Cellular Localization of the Usutu Virus NS5 Protein. Antimicrob Agents Chemother 2019; 64:AAC.01573-19. [PMID: 31685463 PMCID: PMC7187600 DOI: 10.1128/aac.01573-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Usutu virus (USUV) has become increasingly relevant in recent years, with large outbreaks that sporadically have affected humans being reported in wildlife. Similarly to the rest of flaviviruses, USUV contains a positive-sense single-stranded RNA genome which is replicated by the activity of nonstructural protein 5 (NS5). USUV NS5 shows high sequence identity with the remaining viruses in this genus. This permitted us to identify the predicted methyltransferase domain and the RNA-dependent RNA polymerase domain (RdRpD). Owing to their high degree of conservation, viral polymerases are considered priority targets for the development of antiviral compounds. In the present study, we cloned and expressed the entire NS5 and the RdRpD in a heterologous system and used purified preparations for protein characterizations. We determined the optimal reaction conditions by investigating how variations in different physicochemical parameters, such as buffer concentration, temperature, and pH, affect RNA polymerization activity. We also found that USUV polymerase, but not the full-length NS5, exhibits cooperative activity in the synthesis of RNA and that the RdRp activity is not inhibited by sofosbuvir. To further examine the characteristics of USUV polymerase in a more specifically biological context, we have expressed NS5 and the RdRpD in eukaryotic cells and analyzed their subcellular location. NS5 is predominantly found in the cytoplasm; a significant proportion is directed to the nucleus, and this translocation involves nuclear location signals (NLS) located at least between the MTase and RdRpD domains.
Collapse
|
44
|
Tan MJA, Chan KWK, Ng IHW, Kong SYZ, Gwee CP, Watanabe S, Vasudevan SG. The Potential Role of the ZIKV NS5 Nuclear Spherical-Shell Structures in Cell Type-Specific Host Immune Modulation during ZIKV Infection. Cells 2019; 8:cells8121519. [PMID: 31779251 PMCID: PMC6953166 DOI: 10.3390/cells8121519] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 02/07/2023] Open
Abstract
The Zika virus (ZIKV) non-structural protein 5 (NS5) plays multiple viral and cellular roles during infection, with its primary role in virus RNA replication taking place in the cytoplasm. However, immunofluorescence assay studies have detected the presence of ZIKV NS5 in unique spherical shell-like structures in the nuclei of infected cells, suggesting potentially important cellular roles of ZIKV NS5 in the nucleus. Hence ZIKV NS5′s subcellular distribution and localization must be tightly regulated during ZIKV infection. Both ZIKV NS5 expression or ZIKV infection antagonizes type I interferon signaling, and induces a pro-inflammatory transcriptional response in a cell type-specific manner, but the mechanisms involved and the role of nuclear ZIKV NS5 in these cellular functions has not been elucidated. Intriguingly, these cells originate from the brain and placenta, which are also organs that exhibit a pro-inflammatory signature and are known sites of pathogenesis during ZIKV infection in animal models and humans. Here, we discuss the regulation of the subcellular localization of the ZIKV NS5 protein, and its putative role in the induction of an inflammatory response and the occurrence of pathology in specific organs during ZIKV infection.
Collapse
Affiliation(s)
- Min Jie Alvin Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Ivan H. W. Ng
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Sean Yao Zu Kong
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Chin Piaw Gwee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
- Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4022, Australia
- Correspondence: ; Tel.: +65-6516-6718
| |
Collapse
|
45
|
Shimizu H, Saito A, Mikuni J, Nakayama EE, Koyama H, Honma T, Shirouzu M, Sekine SI, Shioda T. Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase. PLoS Negl Trop Dis 2019; 13:e0007894. [PMID: 31738758 PMCID: PMC6886872 DOI: 10.1371/journal.pntd.0007894] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 12/02/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
Dengue is a mosquito-borne viral infection that has spread globally in recent years. Around half of the world's population, especially in the tropics and subtropics, is at risk of infection. Every year, 50-100 million clinical cases are reported, and more than 500,000 patients develop the symptoms of severe dengue infection: dengue haemorrhagic fever and dengue shock syndrome, which threaten life in Asia and Latin America. No antiviral drug for dengue is available. The dengue virus (DENV) non-structural protein 5 (NS5), which possesses the RNA-dependent RNA polymerase (RdRp) activity and is responsible for viral replication and transcription, is an attractive target for anti-dengue drug development. In the present study, 16,240 small-molecule compounds in a fragment library were screened for their capabilities to inhibit the DENV type 2 (DENV2) RdRp activities in vitro. Based on in cellulo antiviral and cytotoxity assays, we selected the compound RK-0404678 with the EC50 value of 6.0 μM for DENV2. Crystallographic analyses revealed two unique binding sites for RK-0404678 within the RdRp, which are conserved in flavivirus NS5 proteins. No resistant viruses emerged after nine rounds of serial passage of DENV2 in the presence of RK-0404678, suggesting the high genetic barrier of this compound to the emergence of a resistant virus. Collectively, RK-0404678 and its binding sites provide a new framework for antiviral drug development.
Collapse
Affiliation(s)
- Hideaki Shimizu
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Akatsuki Saito
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Junko Mikuni
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Emi E. Nakayama
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hiroo Koyama
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, Hirosawa, Wako, Saitama, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Shun-ichi Sekine
- RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- * E-mail: (SS); (TS)
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- * E-mail: (SS); (TS)
| |
Collapse
|
46
|
Sariyer IK, Gordon J, Burdo TH, Wollebo HS, Gianti E, Donadoni M, Bellizzi A, Cicalese S, Loomis R, Robinson JA, Carnevale V, Steiner J, Ozdener MH, Miller AD, Amini S, Klein ML, Khalili K. Suppression of Zika Virus Infection in the Brain by the Antiretroviral Drug Rilpivirine. Mol Ther 2019; 27:2067-2079. [PMID: 31653397 DOI: 10.1016/j.ymthe.2019.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 01/02/2023] Open
Abstract
Zika virus (ZIKV) infection is associated with microcephaly in neonates and Guillain-Barré syndrome in adults. ZIKV produces a class of nonstructural (NS) regulatory proteins that play a critical role in viral transcription and replication, including NS5, which possesses RNA-dependent RNA polymerase (RdRp) activity. Here we demonstrate that rilpivirine (RPV), a non-nucleoside reverse transcriptase inhibitor (NNRTI) used in the treatment of HIV-1 infection, inhibits the enzymatic activity of NS5 and suppresses ZIKV infection and replication in primary human astrocytes. Similarly, other members of the NNRTI family, including etravirine and efavirenz, showed inhibitory effects on viral infection of brain cells. Site-directed mutagenesis identified 14 amino acid residues within the NS5 RdRp domain (AA265-903), which are important for the RPV interaction and the inhibition of NS5 polymerase activity. Administration of RPV to ZIKV-infected interferon-alpha/beta receptor (IFN-A/R) knockout mice improved the clinical outcome and prevented ZIKV-induced mortality. Histopathological examination of the brains from infected animals revealed that RPV reduced ZIKV RNA levels in the hippocampus, frontal cortex, thalamus, and cerebellum. Repurposing of NNRTIs, such as RPV, for the inhibition of ZIKV replication offers a possible therapeutic strategy for the prevention and treatment of ZIKV-associated disease.
Collapse
Affiliation(s)
- Ilker Kudret Sariyer
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Jennifer Gordon
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Tricia H Burdo
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Hassen S Wollebo
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Eleonora Gianti
- Department of Chemistry, Institute for Computational Molecular Science, College of Science and Technology, Temple University, 1901 N. 12(th) Street, Philadelphia, PA 19122, USA
| | - Martina Donadoni
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Anna Bellizzi
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Stephanie Cicalese
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Regina Loomis
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Jake A Robinson
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Vincenzo Carnevale
- Department of Chemistry, Institute for Computational Molecular Science, College of Science and Technology, Temple University, 1901 N. 12(th) Street, Philadelphia, PA 19122, USA
| | - Joseph Steiner
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Mehmet H Ozdener
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA
| | - Andrew D Miller
- College of Veterinary Medicine, Cornell University, T5-006A Veterinary Research Tower, Ithaca, NY 14853, USA
| | - Shohreh Amini
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Michael L Klein
- Department of Chemistry, Institute for Computational Molecular Science, College of Science and Technology, Temple University, 1901 N. 12(th) Street, Philadelphia, PA 19122, USA
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA.
| |
Collapse
|
47
|
Duan Y, Zeng M, Jiang B, Zhang W, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Pan L, Chen S, Cheng A. Flavivirus RNA-Dependent RNA Polymerase Interacts with Genome UTRs and Viral Proteins to Facilitate Flavivirus RNA Replication. Viruses 2019; 11:v11100929. [PMID: 31658680 PMCID: PMC6832647 DOI: 10.3390/v11100929] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022] Open
Abstract
Flaviviruses, most of which are emerging and re-emerging human pathogens and significant public health concerns worldwide, are positive-sense RNA viruses. Flavivirus replication occurs on the ER and is regulated by many mechanisms and factors. NS5, which consists of a C-terminal RdRp domain and an N-terminal methyltransferase domain, plays a pivotal role in genome replication and capping. The C-terminal RdRp domain acts as the polymerase for RNA synthesis and cooperates with diverse viral proteins to facilitate productive RNA proliferation within the replication complex. Here, we provide an overview of the current knowledge of the functions and characteristics of the RdRp, including the subcellular localization of NS5, as well as the network of interactions formed between the RdRp and genome UTRs, NS3, and the methyltransferase domain. We posit that a detailed understanding of RdRp functions may provide a target for antiviral drug discovery and therapeutics.
Collapse
Affiliation(s)
- YanPing Duan
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Miao Zeng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Bowen Jiang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Wei Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - ShaQiu Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - YunYa Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Ling Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - YanLing Yu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Leichang Pan
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu 611130, China.
| |
Collapse
|
48
|
Elshahawi H, Syed Hassan S, Balasubramaniam V. Importance of Zika Virus NS5 Protein for Viral Replication. Pathogens 2019; 8:pathogens8040169. [PMID: 31574966 PMCID: PMC6963216 DOI: 10.3390/pathogens8040169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 01/19/2023] Open
Abstract
Zika virus is the latest addition to an ever-growing list of arboviruses that are causing outbreaks with serious consequences. A few mild cases were recorded between 1960 and 1980 until the first major outbreak in 2007 on Yap Island. This was followed by more severe outbreaks in French Polynesia (2013) and Brazil (2015), which significantly increased both Guillain-Barre syndrome and microcephaly cases. No current vaccines or treatments are available, however, recent studies have taken interest in the NS5 protein which encodes both the viral methyltransferase and RNA-dependent RNA polymerase. This makes it important for viral replication alongside other important functions such as inhibiting the innate immune system thus ensuring virus survival and replication. Structural studies can help design inhibitors, while biochemical studies can help understand the various mechanisms utilized by NS5 thus counteracting them might inhibit or abolish the viral infection. Drug repurposing targeting the NS5 protein has also proven to be an effective tool since hundreds of thousands of compounds can be screened therefore saving time and resources, moreover information on these compounds might already be available especially if they are used to treat other ailments.
Collapse
Affiliation(s)
- Hesham Elshahawi
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya 47500, Selangor, Malaysia.
| | - Sharifah Syed Hassan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya 47500, Selangor, Malaysia.
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya 47500, Selangor, Malaysia.
| | - Vinod Balasubramaniam
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Subang Jaya 47500, Selangor, Malaysia.
| |
Collapse
|
49
|
Valente AP, Moraes AH. Zika virus proteins at an atomic scale: how does structural biology help us to understand and develop vaccines and drugs against Zika virus infection? J Venom Anim Toxins Incl Trop Dis 2019; 25:e20190013. [PMID: 31523227 PMCID: PMC6727858 DOI: 10.1590/1678-9199-jvatitd-2019-0013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In Brazil and in other tropical areas Zika virus infection was directly associated with clinical complications as microcephaly in newborn children whose mothers were infected during pregnancy and the Guillain-Barré syndrome in adults. Recently, research has been focused on developing new vaccines and drug candidates against Zika virus infection since none of those are available. In order to contribute to vaccine and drug development efforts, it becomes important the understanding of the molecular basis of the Zika virus recognition, infection and blockade. To this purpose, it is essential the structural determination of the Zika virus proteins. The genome sequencing of the Zika virus identified ten proteins, being three structural (protein E, protein C and protein prM) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). Together, these proteins are the main targets for drugs and antibody recognition. Here we examine new discoveries on high-resolution structural biology of Zika virus, observing the interactions and functions of its proteins identified via state-of-art structural methodologies as X-ray crystallography, nuclear magnetic resonance spectroscopy and cryogenic electronic microscopy. The aim of the present study is to contribute to the understanding of the structural basis of Zika virus infection at an atomic level and to point out similarities and differences to others flaviviruses.
Collapse
Affiliation(s)
- Ana Paula Valente
- National Center of Magnetic Resonance, Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Adolfo Henrique Moraes
- Department of Chemistry, Institute of Exact Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| |
Collapse
|
50
|
Identification and characterization of Zika virus NS5 RNA-dependent RNA polymerase inhibitors. Int J Antimicrob Agents 2019; 54:502-506. [PMID: 31310806 DOI: 10.1016/j.ijantimicag.2019.07.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 01/05/2023]
Abstract
The current outbreak of Zika virus (ZIKV) is the impetus for novel, safe and efficacious anti-ZIKV agents. ZIKV non-structural protein 5 RNA-dependent RNA polymerase (RdRp) is essential for viral replication and is logically regarded as an attractive drug target. This study used a fluorescence-based polymerase assay to find an anti-infective drug 10-undecenoic acid zinc salt (UA) which could inhibit RdRp activity with a half maximal inhibitory concentration (IC50) of 1.13-1.25 µM. Molecular docking and site-directed mutagenesis analyses identified D535 as the key amino acid in the interaction between RdRp and UA. Importantly, the surface plasmon resonance assay showed that UA had strong direct binding with ZIKV wild-type RdRp and a relatively weak interaction with D535A-RdRp. As a control, the nucleoside inhibitor sofosbuvir triphosphate (PSI-7409) conferred insensitivity to the fluorescence-based RdRp assay and cannot bind directly with RdRp. Moreover, UA showed anti-ZIKV activity comparable to sofosbuvir. All these results indicate that UA is likely to be a promising lead compound against ZIKV, exhibiting a different mechanism than sofosbuvir.
Collapse
|