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Bonomini A, Mercorelli B, Loregian A. Antiviral strategies against influenza virus: an update on approved and innovative therapeutic approaches. Cell Mol Life Sci 2025; 82:75. [PMID: 39945883 PMCID: PMC11825441 DOI: 10.1007/s00018-025-05611-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 01/27/2025] [Accepted: 02/02/2025] [Indexed: 02/16/2025]
Abstract
Influenza viruses still represent a great concern for Public Health by causing yearly seasonal epidemics and occasionally worldwide pandemics. Moreover, spillover events at the animal-human interface are becoming more frequent nowadays, also involving animal species not previously found as reservoirs. To restrict the effects of influenza virus epidemics, especially in at-risk population, and to prepare a drug arsenal for possible future pandemics, researchers worldwide have been working on the development of antiviral strategies since the 80's of the last century. One of the main obstacles is the considerable genomic variability of influenza viruses, which constantly poses the issues of drug-resistance emergence and immune evasion. This review summarizes the approved therapeutics for clinical management of influenza, promising new anti-flu compounds and monoclonal antibodies currently undergoing clinical evaluation, and molecules with efficacy against influenza virus in preclinical studies. Moreover, we discuss some innovative anti-influenza therapeutic approaches such as combination therapies and targeted protein degradation. Given the limited number of drugs approved for influenza treatment, there is a still strong need for novel potent anti-influenza drugs endowed with a high barrier to drug resistance and broad-spectrum activity against influenza viruses of animal origin that may be responsible of future large outbreaks and pandemics.
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Affiliation(s)
- Anna Bonomini
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Padua, Italy.
- Microbiology and Virology Unit, Padua University Hospital, Padua, Italy.
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2
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Liang H, Zhang Y, Sun W, Xiao X, Zhao X, Tan B, Zhang J, Song X, He Z, Ye L. Identification of a Novel Alkaloid Zj6-11 as a Potent Inhibitor of Influenza Virus Infection via Repression of Virus-Induced Mitochondria-Dependent Apoptosis. J Med Virol 2025; 97:e70230. [PMID: 39921608 DOI: 10.1002/jmv.70230] [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: 09/12/2024] [Revised: 01/23/2025] [Accepted: 01/29/2025] [Indexed: 02/10/2025]
Abstract
Influenza A virus (IAV) remains a major global public health threat, especially with the emergence of antiviral resistance, highlighting the urgent need for novel therapeutics. Alkaloids are known for their antiviral properties, and chemical synthesis has become a key strategy in developing new alkaloid compounds. In this study, we synthesized a series of novel alkaloids using the Ugi reaction and assessed their antiviral potential and mechanisms. Through screening and validation, Zj6-11 was identified as a promising compound that effectively inhibits IAV infection in vitro. Molecular docking and binding affinity assays showed that Zj6-11 binds with high affinity to IAV nucleoprotein (NP) and inhibits its interaction with nucleic acids. Further, in vitro nuclear translocation assays confirmed that Zj6-11 suppresses NP nuclear import. Mechanistically, Zj6-11 significantly inhibits IAV-induced apoptosis and mitigates mitochondrial membrane potential dysfunction. Zj6-11 also inhibits cytochrome c release, reduces the expression of cleaved Caspase-9 and Caspase-3, and suppresses IAV-induced apoptosis-inducing factor (Aif) expression, suppressing IAV-induced mitochondrial apoptosis. More importantly, Zj6-11 plays a crucial role in protecting mice from IAV infection and reducing IAV pathogenicity. Our study provides mechanistic insights into Zj6-11's control of IAV infection in vitro and in vivo, offering new perspectives for antiviral therapy development.
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Affiliation(s)
- Hanbai Liang
- Department of Immunology, International Cancer Center, College of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Ying Zhang
- Department of Immunology, International Cancer Center, College of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Wenhao Sun
- Department of Immunology, International Cancer Center, College of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Xiaomei Xiao
- Department of Immunology, International Cancer Center, College of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Xiwen Zhao
- Department of Immunology, International Cancer Center, College of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Bin Tan
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
| | - Jian Zhang
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
| | - Xun Song
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Zhengdan He
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Liang Ye
- Department of Immunology, International Cancer Center, College of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
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Panthi S, Hong JY, Satange R, Yu CC, Li LY, Hou MH. Antiviral drug development by targeting RNA binding site, oligomerization and nuclear export of influenza nucleoprotein. Int J Biol Macromol 2024; 282:136996. [PMID: 39486729 DOI: 10.1016/j.ijbiomac.2024.136996] [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: 08/12/2024] [Revised: 10/23/2024] [Accepted: 10/26/2024] [Indexed: 11/04/2024]
Abstract
The quasispecies of the influenza virus poses a significant challenge for developing effective therapies. Current antiviral drugs such as oseltamivir, zanamivir, peramivir and baloxavir marboxil along with seasonal vaccines have limitations due to viral variability caused by antigenic drift and shift as well as the development of drug resistance. Therefore, there is a clear need for novel antiviral agents targeting alternative mechanisms, either independently or in combination with existing modalities, to reduce the impact of influenza virus-related infections. The influenza nucleoprotein (NP) is a key component of the viral ribonucleoprotein complex. The multifaceted nature of the NP makes it an attractive target for antiviral intervention. Recent reports have identified inhibitors that specifically target this protein. Recognizing the importance of developing influenza treatments for potential pandemics, this review explores the structural and functional aspects of NP and highlights its potential as an emerging target for anti-influenza drugs. We discuss various strategies for targeting NP, including RNA binding, oligomerization, and nuclear export, and also consider the potential of NP-based vaccines. Overall, this review provides insights into recent developments and future perspectives on targeting influenza NP for antiviral therapies.
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Affiliation(s)
- Sankar Panthi
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Jhen-Yi Hong
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Ching-Ching Yu
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Long-Yuan Li
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
| | - Ming-Hon Hou
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan; Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan; Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan.
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Du S, Liu X, Hu X, Zhan P. Viral Protein Dimerization Quality Control: A Design Strategy for a Potential Viral Inhibitor. J Med Chem 2024; 67:16951-16966. [PMID: 39303015 DOI: 10.1021/acs.jmedchem.4c01540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The global pharmaceutical market has been profoundly impacted by the coronavirus pandemic, leading to an increased demand for specific drugs. Consequently, drug resistance has prompted continuous innovation in drug design strategies to effectively combat resistant pathogens or disease variants. Protein dimers play crucial roles in vivo, including catalytic reactions, signal transduction, and structural stability. The site of action for protein dimerization modulators typically does not reside within the active site of the protein, thereby potentially impeding resistance development. Therefore, harnessing viral protein dimerization modulators could represent a promising avenue for combating viral infections. In this Perspective, we provide a detailed introduction to the design principles and applications of dimerization modulators in antiviral research. Furthermore, we analyze various representative examples to elucidate their modes of action while presenting our perspective on dimerization modulators along with the opportunities and challenges associated with this groundbreaking area of investigation.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
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Rabaan AA, Halwani MA, Garout M, Alotaibi J, AlShehail BM, Alotaibi N, Almuthree SA, Alshehri AA, Alshahrani MA, Othman B, Alqahtani A, Alissa M. Exploration of phytochemical compounds against Marburg virus using QSAR, molecular dynamics, and free energy landscape. Mol Divers 2024; 28:3261-3278. [PMID: 37925643 DOI: 10.1007/s11030-023-10753-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023]
Abstract
Marburg virus disease (MVD) is caused by the Marburg virus, a one-of-a-kind zoonotic RNA virus from the genus Filovirus. Thus, this current study employed AI-based QSAR and molecular docking-based virtual screening for identifying potential binders against the target protein (nucleoprotein (NP)) of the Marburg virus. A total of 2727 phytochemicals were used for screening, out of which the top three compounds (74977521, 90470472, and 11953909) were identified based on their predicted bioactivity (pIC50) and binding score (< - 7.4 kcal/mol). Later, MD simulation in triplicates and trajectory analysis were performed which showed that 11953909 and 74977521 had the most stable and consistent complex formations and had the most significant interactions with the highest number of hydrogen bonds. PCA (principal component analysis) and FEL (free energy landscape) analysis indicated that these compounds had favourable energy states for most of the conformations. The total binding free energy of the compounds using the MM/GBSA technique showed that 11953909 (ΔGTOTAL = - 30.78 kcal/mol) and 74977521 (ΔGTOTAL = - 30 kcal/mol) had the highest binding affinity with the protein. Overall, this in silico pipeline proposed that the phytochemicals 11953909 and 74977521 could be the possible binders of NP. This study aimed to find phytochemicals inhibiting the protein's function and potentially treating MVD.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia.
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, 4781, Al Baha, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Jawaher Alotaibi
- Infectious diseases Unit, Department of Medicine, King Faisal Specialist Hospital and Research Center, 11564, Riyadh, Saudi Arabia
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Nouf Alotaibi
- Clinical pharmacy Department, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Souad A Almuthree
- Department of Infectious Disease, King Abdullah Medical City, 43442, Makkah, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 61441, Najran, Saudi Arabia
| | - Basim Othman
- Department of Public Health, Faculty of Applied Medical Sciences, Al Baha University, 65779, Al Baha, Saudi Arabia
| | - Abdulaziz Alqahtani
- Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, 61321, Abha, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia.
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He Y, Shen M, Wang X, Yin A, Liu B, Zhu J, Zhang Z. Suppression of Interferon Response and Antiviral Strategies of Bunyaviruses. Trop Med Infect Dis 2024; 9:205. [PMID: 39330894 PMCID: PMC11435552 DOI: 10.3390/tropicalmed9090205] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/28/2024] [Accepted: 09/05/2024] [Indexed: 09/28/2024] Open
Abstract
The order Bunyavirales belongs to the class of Ellioviricetes and is classified into fourteen families. Some species of the order Bunyavirales pose potential threats to human health. The continuously increasing research reveals that various viruses within this order achieve immune evasion in the host through suppressing interferon (IFN) response. As the types and nodes of the interferon response pathway are continually updated or enriched, the IFN suppression mechanisms and target points of different virus species within this order are also constantly enriched and exhibit variations. For instance, Puumala virus (PUUV) and Tula virus (TULV) can inhibit IFN response through their functional NSs inhibiting downstream factor IRF3 activity. Nevertheless, the IFN suppression mechanisms of Dabie bandavirus (DBV) and Guertu virus (GTV) are mostly mediated by viral inclusion bodies (IBs) or filamentous structures (FSs). Currently, there are no effective drugs against several viruses belonging to this order that pose significant threats to society and human health. While the discovery, development, and application of antiviral drugs constitute a lengthy process, our focus on key targets in the IFN response suppression process of the virus leads to potential antiviral strategies, which provide references for both basic research and practical applications.
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Affiliation(s)
- Yingying He
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; (Y.H.); (M.S.); (X.W.); (A.Y.); (B.L.)
- Department of Clinical Medicine, Anhui Medical University, Hefei 230032, China
| | - Min Shen
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; (Y.H.); (M.S.); (X.W.); (A.Y.); (B.L.)
- Department of Clinical Medicine, Anhui Medical University, Hefei 230032, China
| | - Xiaohe Wang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; (Y.H.); (M.S.); (X.W.); (A.Y.); (B.L.)
- Department of Clinical Medicine, Anhui Medical University, Hefei 230032, China
| | - Anqi Yin
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; (Y.H.); (M.S.); (X.W.); (A.Y.); (B.L.)
- Department of Clinical Medicine, Anhui Medical University, Hefei 230032, China
| | - Bingyan Liu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; (Y.H.); (M.S.); (X.W.); (A.Y.); (B.L.)
| | - Jie Zhu
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; (Y.H.); (M.S.); (X.W.); (A.Y.); (B.L.)
| | - Zhenhua Zhang
- Institute of Clinical Virology, Department of Infectious Diseases, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China; (Y.H.); (M.S.); (X.W.); (A.Y.); (B.L.)
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Dong M, Wang Y, Li P, Chen Z, Anirudhan V, Cui Q, Rong L, Du R. Allopregnanolone targets nucleoprotein as a novel influenza virus inhibitor. Virol Sin 2023; 38:931-939. [PMID: 37741571 PMCID: PMC10786660 DOI: 10.1016/j.virs.2023.09.003] [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: 06/11/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023] Open
Abstract
Influenza A virus (IAV) poses a global public health concern and remains an imminent threat to human health. Emerging antiviral resistance to the currently approved influenza drugs emphasizes the urgent need for new therapeutic entities against IAV. Allopregnanolone (ALLO) is a natural product that has been approved as an antidepressant drug. In the present study, we repurposed ALLO as a novel inhibitor against IAVs. Mechanistic studies demonstrated that ALLO inhibited virus replication by interfering with the nucleus translocation of viral nucleoprotein (NP). In addition, ALLO showed significant synergistic activity with compound 16, a hemagglutinin inhibitor of IAVs. In summary, we have identified ALLO as a novel influenza virus inhibitor targeting NP, providing a promising candidate that deserves further investigation as a useful anti-influenza strategy in the future.
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Affiliation(s)
- Meiyue Dong
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Yanyan Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Ping Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Zinuo Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Varada Anirudhan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, 60612, USA
| | - Qinghua Cui
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China; Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, 266122, China.
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, 60612, USA.
| | - Ruikun Du
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China; Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, 266122, China.
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Zhang Y, Xu WF, Yu Y, Zhang Q, Huang L, Hao C, Shao CL, Wang W. Inhibition of influenza A virus replication by a marine derived quinolone alkaloid targeting virus nucleoprotein. J Med Virol 2023; 95:e28499. [PMID: 36653877 DOI: 10.1002/jmv.28499] [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: 10/19/2022] [Revised: 12/14/2022] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
Owing to the emergence of drug resistance and high morbidity and mortality, the need for novel anti-influenza A virus (IAV) drugs with divergent targets is highly sought after. Herein, a novel quinolone alkaloid (QLA) derived from marine fungus was discovered with broad-spectrum anti-IAV activities with low toxicity. Distinct from current anti-IAV drugs, QLA may block virus replication and viral RNA (vRNA) export from the nucleus by targeting virus nucleoprotein (NP). QLA can block the binding of chromosome region maintenance 1 to nuclear export signal 3 of NP to inhibit the nuclear export of NP and vRNP. QLA may also affect vRNP assembly by interfering with the binding of NP to RNA rather than NP oligomerization. Arg305 and Phe488-Gly490 may be required for the interaction between QLA and NP, and the binding pocket around these amino acids may be a promising target for anti-IAV drugs. Importantly, oral administration of QLA can protect the mice against IAV-induced death and weight loss, superior to the effects of the clinical drug oseltamivir. In summary, the marine derived compound QLA has the potential to be developed into a novel anti-IAV agent targeting virus NP protein in the future.
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Affiliation(s)
- Yang Zhang
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Wei-Feng Xu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yunjia Yu
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qun Zhang
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lianghao Huang
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China
| | - Cui Hao
- Medical Research Center, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chang-Lun Shao
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wei Wang
- School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Hou L, Zhang Y, Ju H, Cherukupalli S, Jia R, Zhang J, Huang B, Loregian A, Liu X, Zhan P. Contemporary medicinal chemistry strategies for the discovery and optimization of influenza inhibitors targeting vRNP constituent proteins. Acta Pharm Sin B 2022; 12:1805-1824. [PMID: 35847499 PMCID: PMC9279641 DOI: 10.1016/j.apsb.2021.11.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/02/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Influenza is an acute respiratory infectious disease caused by the influenza virus, affecting people globally and causing significant social and economic losses. Due to the inevitable limitations of vaccines and approved drugs, there is an urgent need to discover new anti-influenza drugs with different mechanisms. The viral ribonucleoprotein complex (vRNP) plays an essential role in the life cycle of influenza viruses, representing an attractive target for drug design. In recent years, the functional area of constituent proteins in vRNP are widely used as targets for drug discovery, especially the PA endonuclease active site, the RNA-binding site of PB1, the cap-binding site of PB2 and the nuclear export signal of NP protein. Encouragingly, the PA inhibitor baloxavir has been marketed in Japan and the United States, and several drug candidates have also entered clinical trials, such as favipiravir. This article reviews the compositions and functions of the influenza virus vRNP and the research progress on vRNP inhibitors, and discusses the representative drug discovery and optimization strategies pursued.
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Abstract
Influenza viruses are one of the leading causes of respiratory tract infections in humans and their newly emerging and re-emerging virus strains are responsible for seasonal epidemics and occasional pandemics, leading to a serious threat to global public health systems. The poor clinical outcome and pathogenesis during influenza virus infection in humans and animal models are often associated with elevated proinflammatory cytokines and chemokines production, which is also known as hypercytokinemia or "cytokine storm", that precedes acute respiratory distress syndrome (ARDS) and often leads to death. Although we still do not fully understand the complex nature of cytokine storms, the use of immunomodulatory drugs is a promising approach for treating hypercytokinemia induced by an acute viral infection, including highly pathogenic avian influenza virus infection and Coronavirus Disease 2019 (COVID-19). This review aims to discuss the immune responses and cytokine storm pathology induced by influenza virus infection and also summarize alternative experimental strategies for treating hypercytokinemia caused by influenza virus.
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Affiliation(s)
- Fanhua Wei
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China.,College of Agriculture, Ningxia University, Yinchuan, China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, School of Biomedical Sciences, Shandong University, Jinan, China
| | - Yujiong Wang
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China.,College of Life Science, Ningxia University, Yinchuan, China
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Yang F, Pang B, Lai KK, Cheung NN, Dai J, Zhang W, Zhang J, Chan KH, Chen H, Sze KH, Zhang H, Hao Q, Yang D, Yuen KY, Kao RY. Discovery of a Novel Specific Inhibitor Targeting Influenza A Virus Nucleoprotein with Pleiotropic Inhibitory Effects on Various Steps of the Viral Life Cycle. J Virol 2021; 95:e01432-20. [PMID: 33627391 PMCID: PMC8104107 DOI: 10.1128/jvi.01432-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/29/2021] [Indexed: 11/23/2022] Open
Abstract
Influenza A viruses (IAVs) continue to pose an imminent threat to humans due to annual influenza epidemic outbreaks and episodic pandemics with high mortality rates. In this context, the suboptimal vaccine coverage and efficacy, coupled with recurrent events of viral resistance against a very limited antiviral portfolio, emphasize an urgent need for new additional prophylactic and therapeutic options, including new antiviral targets and drugs with new mechanisms of action to prevent and treat influenza virus infection. Here, we characterized a novel influenza A virus nucleoprotein (NP) inhibitor, FA-6005, that inhibited a broad spectrum of human pandemic and seasonal influenza A and B viruses in vitro and protects mice against lethal influenza A virus challenge. The small molecule FA-6005 targeted a conserved NP I41 domain and acted as a potentially broad, multimechanistic anti-influenza virus therapeutic since FA-6005 suppressed influenza virus replication and perturbed intracellular trafficking of viral ribonucleoproteins (vRNPs) from early to late stages. Cocrystal structures of the NP/FA-6005 complex reconciled well with concurrent mutational studies. This study provides the first line of direct evidence suggesting that the newly identified NP I41 pocket is an attractive target for drug development that inhibits multiple functions of NP. Our results also highlight FA-6005 as a promising candidate for further development as an antiviral drug for the treatment of IAV infection and provide chemical-level details for inhibitor optimization.IMPORTANCE Current influenza antivirals have limitations with regard to their effectiveness and the potential emergence of resistance. Therefore, there is an urgent need for broad-spectrum inhibitors to address the considerable challenges posed by the rapid evolution of influenza viruses that limit the effectiveness of vaccines and lead to the emergence of antiviral drug resistance. Here, we identified a novel influenza A virus NP antagonist, FA-6005, with broad-spectrum efficacy against influenza viruses, and our study presents a comprehensive study of the mode of action of FA-6005 with the crystal structure of the compound in complex with NP. The influenza virus inhibitor holds promise as an urgently sought-after therapeutic option offering a mechanism of action complementary to existing antiviral drugs for the treatment of influenza virus infection and should further aid in the development of universal therapeutics.
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Affiliation(s)
- Fang Yang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Bo Pang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Kin Kui Lai
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Nam Nam Cheung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jun Dai
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Weizhe Zhang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Jinxia Zhang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Honglin Chen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- Research Center of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Kong-Hung Sze
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hongmin Zhang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen, China
- SUSTech-HKU Joint Laboratories for Matrix Biology and Diseases, Southern University of Science and Technology, Shenzhen, China
| | - Quan Hao
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Dan Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- Research Center of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Richard Y Kao
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- Research Center of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
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12
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Eguida M, Rognan D. A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design. J Med Chem 2020; 63:7127-7142. [DOI: 10.1021/acs.jmedchem.0c00422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Merveille Eguida
- UMR 7200 CNRS-Université de Strasbourg, Laboratoire d’Innovation Thérapeutique, 67400 Illkirch, France
| | - Didier Rognan
- UMR 7200 CNRS-Université de Strasbourg, Laboratoire d’Innovation Thérapeutique, 67400 Illkirch, France
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13
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Makau JN, Watanabe K, Otaki H, Mizuta S, Ishikawa T, Kamatari YO, Nishida N. A Quinolinone Compound Inhibiting the Oligomerization of Nucleoprotein of Influenza A Virus Prevents the Selection of Escape Mutants. Viruses 2020; 12:v12030337. [PMID: 32204549 PMCID: PMC7150793 DOI: 10.3390/v12030337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/10/2020] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of resistance to currently available anti-influenza drugs has heightened the need for antivirals with novel mechanisms of action. The influenza A virus (IAV) nucleoprotein (NP) is highly conserved and essential for the formation of viral ribonucleoprotein (vRNP), which serves as the template for replication and transcription. Recently, using in silico screening, we identified an antiviral compound designated NUD-1 (a 4-hydroxyquinolinone derivative) as a potential inhibitor of NP. In this study, we further analyzed the interaction between NUD-1 and NP and found that the compound interferes with the oligomerization of NP, which is required for vRNP formation, leading to the suppression of viral transcription, protein synthesis, and nuclear export of NP. We further assessed the selection of resistant variants by serially passaging a clinical isolate of the 2009 H1N1 pandemic influenza virus in the presence of NUD-1 or oseltamivir. NUD-1 did not select for resistant variants after nine passages, whereas oseltamivir selected for resistant variants after five passages. Our data demonstrate that NUD-1 interferes with the oligomerization of NP and less likely induces drug-resistant variants than oseltamivir; hence, it is a potential lead compound for the development of novel anti-influenza drugs.
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Affiliation(s)
- Juliann Nzembi Makau
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (J.N.M.); (N.N.)
| | - Ken Watanabe
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (J.N.M.); (N.N.)
- Department of Lifestyle Design, Faculty of Human Ecology, Yasuda Women’s University, 6-13-1 Yasuhigashi, Asaminami ward, Hiroshima 731-0153, Japan
- Correspondence: ; Tel.: +81-82-878-9139
| | - Hiroki Otaki
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (H.O.); (S.M.)
| | - Satoshi Mizuta
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (H.O.); (S.M.)
| | - Takeshi Ishikawa
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan;
| | - Yuji O. Kamatari
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan;
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (J.N.M.); (N.N.)
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14
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Zheng W, Fan W, Zhang S, Jiao P, Shang Y, Cui L, Mahesutihan M, Li J, Wang D, Gao GF, Sun L, Liu W. Naproxen Exhibits Broad Anti-influenza Virus Activity in Mice by Impeding Viral Nucleoprotein Nuclear Export. Cell Rep 2019; 27:1875-1885.e5. [PMID: 31067470 DOI: 10.1016/j.celrep.2019.04.053] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/01/2019] [Accepted: 04/11/2019] [Indexed: 12/16/2022] Open
Abstract
Naproxen is a non-steroidal anti-inflammatory drug that has previously been shown to exert antiviral activity against influenza A virus by inhibiting nucleoprotein (NP) binding to RNA. Here, we show that naproxen is a potential broad, multi-mechanistic anti-influenza virus therapeutic, as it inhibits influenza B virus replication both in vivo and in vitro. The anti-influenza B virus activity of naproxen is more efficient than that of the commonly used neuraminidase inhibitor oseltamivir in mice. Furthermore, the NP of influenza B virus (BNP) has a higher binding affinity to naproxen than influenza A virus NP (ANP). Specifically, naproxen targets the NP at residues F209 (BNP) and Y148 (ANP). This interaction antagonizes the nuclear export of NP normally mediated by the host export protein CRM1. This study reveals a crucial mechanism of broad-spectrum anti-influenza virus activity of naproxen, suggesting that the existing drug naproxen may be used as an anti-influenza drug.
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Affiliation(s)
- Weinan Zheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenhui Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengtao Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresourses & Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University, Nanning 530004, China
| | - Yingli Shang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Liang Cui
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Madina Mahesutihan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dayan Wang
- Chinese National Influenza Center (CNIC), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Chinese National Influenza Center (CNIC), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Cross ST, Michalski D, Miller MR, Wilusz J. RNA regulatory processes in RNA virus biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1536. [PMID: 31034160 PMCID: PMC6697219 DOI: 10.1002/wrna.1536] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Numerous post‐transcriptional RNA processes play a major role in regulating the quantity, quality and diversity of gene expression in the cell. These include RNA processing events such as capping, splicing, polyadenylation and modification, but also aspects such as RNA localization, decay, translation, and non‐coding RNA‐associated regulation. The interface between the transcripts of RNA viruses and the various RNA regulatory processes in the cell, therefore, has high potential to significantly impact virus gene expression, regulation, cytopathology and pathogenesis. Furthermore, understanding RNA biology from the perspective of an RNA virus can shed considerable light on the broad impact of these post‐transcriptional processes in cell biology. Thus the goal of this article is to provide an overview of the richness of cellular RNA biology and how RNA viruses use, usurp and/or avoid the associated machinery to impact the outcome of infection. This article is categorized under:RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Daniel Michalski
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Megan R Miller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado
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16
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Meng W, Wang XJ, Wang HCR. Targeting nuclear proteins for control of viral replication. Crit Rev Microbiol 2019; 45:495-513. [DOI: 10.1080/1040841x.2018.1553848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wen Meng
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hwa-Chain Robert Wang
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, The University of Tennessee, Knoxville, USA
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17
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Chenodeoxycholic Acid from Bile Inhibits Influenza A Virus Replication via Blocking Nuclear Export of Viral Ribonucleoprotein Complexes. Molecules 2018; 23:molecules23123315. [PMID: 30558117 PMCID: PMC6321071 DOI: 10.3390/molecules23123315] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 11/27/2022] Open
Abstract
Influenza A virus (IAV) infection is still a major global threat for humans, especially for the risk groups: young children and the elderly. The currently licensed antiviral drugs target viral factors and are prone to viral resistance. In recent years, a few endogenous small molecules from host, such as estradiol and omega-3 polyunsaturated fatty acid (PUFA)-derived lipid mediator protection D1 (PD1), were demonstrated to be capable of inhibiting IAV infection. Chenodeoxycholic acid (CDCA), one of the main primary bile acids, is synthesized from cholesterol in the liver and classically functions in emulsification and absorption of dietary fats. Clinically, CDCA has been used in the treatment of patients with cholesterol gallstones for more than five decades. In this study, we showed that CDCA attenuated the replication of three subtypes of influenza A virus, including a highly pathogenic H5N1 strain, in A549 and MDCK cell cultures with IC50 ranging from 5.5 to 11.5 μM. Mechanistically, CDCA effectively restrained the nuclear export of viral ribonucleoprotein (vRNP) complexes. In conclusion, as an endogenous physiological small molecule, CDCA can inhibit IAV replication in vitro, at least in part, by blocking vRNP nuclear export, and affords further studies for development as a potential antiviral agent against IAV infections.
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18
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Ehrt C, Brinkjost T, Koch O. A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs). PLoS Comput Biol 2018; 14:e1006483. [PMID: 30408032 PMCID: PMC6224041 DOI: 10.1371/journal.pcbi.1006483] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 09/02/2018] [Indexed: 11/24/2022] Open
Abstract
The automated comparison of protein-ligand binding sites provides useful insights into yet unexplored site similarities. Various stages of computational and chemical biology research can benefit from this knowledge. The search for putative off-targets and the establishment of polypharmacological effects by comparing binding sites led to promising results for numerous projects. Although many cavity comparison methods are available, a comprehensive analysis to guide the choice of a tool for a specific application is wanting. Moreover, the broad variety of binding site modeling approaches, comparison algorithms, and scoring metrics impedes this choice. Herein, we aim to elucidate strengths and weaknesses of binding site comparison methodologies. A detailed benchmark study is the only possibility to rationalize the selection of appropriate tools for different scenarios. Specific evaluation data sets were developed to shed light on multiple aspects of binding site comparison. An assembly of all applied benchmark sets (ProSPECCTs–Protein Site Pairs for the Evaluation of Cavity Comparison Tools) is made available for the evaluation and optimization of further and still emerging methods. The results indicate the importance of such analyses to facilitate the choice of a methodology that complies with the requirements of a specific scientific challenge. Binding site similarities are useful in the context of promiscuity prediction, drug repurposing, the analysis of protein-ligand and protein-protein complexes, function prediction, and further fields of general interest in chemical biology and biochemistry. Many years of research have led to the development of a multitude of methods for binding site analysis and comparison. On the one hand, their availability supports research. On the other hand, the huge number of methods hampers the efficient selection of a specific tool. Our research is dedicated to the analysis of different cavity comparison tools. We use several binding site data sets to establish guidelines which can be applied to ensure a successful application of comparison methods by circumventing potential pitfalls.
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Affiliation(s)
- Christiane Ehrt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Tobias Brinkjost
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Computer Science, TU Dortmund University, Dortmund, Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- * E-mail: ,
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19
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Liu T, Liu M, Chen F, Chen F, Tian Y, Huang Q, Liu S, Yang J. A Small-Molecule Compound Has Anti-influenza A Virus Activity by Acting as a ‘‘PB2 Inhibitor”. Mol Pharm 2018; 15:4110-4120. [DOI: 10.1021/acs.molpharmaceut.8b00531] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Teng Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Miaomiao Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feimin Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Fangzhao Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qi Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jie Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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20
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Dilly S, Fotso Fotso A, Lejal N, Zedda G, Chebbo M, Rahman F, Companys S, Bertrand HC, Vidic J, Noiray M, Alessi MC, Tarus B, Quideau S, Riteau B, Slama-Schwok A. From Naproxen Repurposing to Naproxen Analogues and Their Antiviral Activity against Influenza A Virus. J Med Chem 2018; 61:7202-7217. [DOI: 10.1021/acs.jmedchem.8b00557] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sébastien Dilly
- Gustave Roussy Institute, Paris Saclay University, UMR8200 CNRS, 94805 Villejuif, France
| | - Aurélien Fotso Fotso
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Nathalie Lejal
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
| | - Gloria Zedda
- Bordeaux University, ISM (CNRS-UMR 5255), 33405 Talence, France
| | - Mohamad Chebbo
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Fryad Rahman
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Simon Companys
- Bordeaux University, ISM (CNRS-UMR 5255), 33405 Talence, France
| | | | - Jasmina Vidic
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
| | - Magali Noiray
- Paris Sud University, Paris Saclay University, UMS IPSIT, Intermol, 92290 Châtenay-Malabry, France
| | | | - Bogdan Tarus
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
| | | | - Béatrice Riteau
- Aix Marseille University, INSERM, INRA, NORT, UMR 1260/1062, 13007 Marseille, France
| | - Anny Slama-Schwok
- Gustave Roussy Institute, Paris Saclay University, UMR8200 CNRS, 94805 Villejuif, France
- Paris Saclay University, UR 892, INRA, 78352 Jouy en Josas, France
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21
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White KM, Abreu P, Wang H, De Jesus PD, Manicassamy B, García-Sastre A, Chanda SK, DeVita RJ, Shaw ML. Broad Spectrum Inhibitor of Influenza A and B Viruses Targeting the Viral Nucleoprotein. ACS Infect Dis 2018; 4:146-157. [PMID: 29268608 PMCID: PMC6145453 DOI: 10.1021/acsinfecdis.7b00120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
S119 was a top hit from an ultrahigh throughput screen performed to identify novel inhibitors of influenza virus replication. It showed a potent antiviral effect (50% inhibitory concentration, IC50 = 20 nM) and no detectable cytotoxicity (50% cytotoxic concentration, CC50 > 500 μM) to yield a selectivity index greater than 25 000. Upon investigation, we found that S119 selected for resistant viruses carrying mutations in the viral nucleoprotein (NP). These resistance mutations highlight a likely S119 binding site overlapping with but not identical to that found for the compound nucleozin. Mechanism of action studies revealed that S119 affects both the oligomerization state and cellular localization of the NP protein which has an impact on viral transcription, replication, and protein expression. Through a hit-to-lead structure-activity relationship (SAR) study, we found an analog of S119, named S119-8, which had increased breadth of inhibition against influenza A and B viruses accompanied by only a small loss in potency. Finally, in vitro viral inhibition assays showed a synergistic relationship between S119-8 and oseltamivir when they were combined, indicating the potential for future drug cocktails.
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Affiliation(s)
- Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Pablo Abreu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Hui Wang
- Department of Pharmacological Sciences, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Paul D. De Jesus
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Balaji Manicassamy
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Robert J. DeVita
- Department of Pharmacological Sciences, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Megan L. Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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22
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Huang F, Chen J, Zhang J, Tan L, Lu G, Luo Y, Pan T, Liang J, Li Q, Luo B, Zhang H, Lu G. Identification of a novel compound targeting the nuclear export of influenza A virus nucleoprotein. J Cell Mol Med 2017; 22:1826-1839. [PMID: 29193684 PMCID: PMC5824420 DOI: 10.1111/jcmm.13467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/23/2017] [Indexed: 12/25/2022] Open
Abstract
Although antiviral drugs are available for the treatment of influenza infection, it is an urgent requirement to develop new antiviral drugs regarding the emergence of drug‐resistant viruses. The nucleoprotein (NP) is conserved among all influenza A viruses (IAVs) and has no cellular equivalent. Therefore, NP is an ideal target for the development of new IAV inhibitors. In this study, we identified a novel anti‐influenza compound, ZBMD‐1, from a library of 20,000 compounds using cell‐based influenza A infection assays. We found that ZBMD‐1 inhibited the replication of H1N1 and H3N2 influenza A virus strains in vitro, with an IC50 ranging from 0.41–1.14 μM. Furthermore, ZBMD‐1 inhibited the polymerase activity and specifically impaired the nuclear export of NP. Further investigation indicated that ZBMD‐1 binds to the nuclear export signal 3 (NES3) domain and the dimer interface of the NP pocket. ZBMD‐1 also protected mice that were challenged with lethal doses of A/PR/8/1934 (H1N1) virus, effectively relieving lung histopathology changes, as well as strongly inhibiting the expression of pro‐inflammatory cytokines/chemokines, without inducing toxicity effects in mice. These results suggest that ZBMD‐1 is a promising anti‐influenza compound which can be further investigated as a useful strategy against IAVs in the future.
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Affiliation(s)
- Feng Huang
- Department of Respiration, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jingliang Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Junsong Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Likai Tan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Gui Lu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yongjie Luo
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ting Pan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Juanran Liang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Qianwen Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Baohong Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Gen Lu
- Department of Respiration, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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23
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Shin WJ, Seong BL. Type II transmembrane serine proteases as potential target for anti-influenza drug discovery. Expert Opin Drug Discov 2017; 12:1139-1152. [DOI: 10.1080/17460441.2017.1372417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Woo-Jin Shin
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
- Vaccine Translational Research Center, Yonsei University, Seoul, South Korea
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24
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Hu Y, Sneyd H, Dekant R, Wang J. Influenza A Virus Nucleoprotein: A Highly Conserved Multi-Functional Viral Protein as a Hot Antiviral Drug Target. Curr Top Med Chem 2017; 17:2271-2285. [PMID: 28240183 DOI: 10.2174/1568026617666170224122508] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 01/25/2023]
Abstract
Prevention and treatment of influenza virus infection is an ongoing unmet medical need. Each year, thousands of deaths and millions of hospitalizations are attributed to influenza virus infection, which poses a tremendous health and economic burden to the society. Aside from the annual influenza season, influenza viruses also lead to occasional influenza pandemics as a result of emerging or re-emerging influenza strains. Influenza viruses are RNA viruses that exist in quasispecies, meaning that they have a very diverse genetic background. Such a feature creates a grand challenge in devising therapeutic intervention strategies to inhibit influenza virus replication, as a single agent might not be able to inhibit all influenza virus strains. Both classes of currently approved anti-influenza drugs have limitations: the M2 channel blockers amantadine and rimantadine are no longer recommended for use in the U.S. due to predominant drug resistance, and resistance to the neuraminidase inhibitor oseltamivir is continuously on the rise. In pursuing the next generation of antiviral drugs with broad-spectrum activity and higher genetic barrier of drug resistance, the influenza virus nucleoprotein (NP) stands out as a high-profile drug target. This review summarizes recent developments in designing inhibitors targeting influenza NP and their mechanisms of action.
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Affiliation(s)
- Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
| | - Hannah Sneyd
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
| | - Raphael Dekant
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, the University of Arizona, Tucson, AZ, United States
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25
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van de Wakker SI, Fischer MJ, Oosting RS. New drug-strategies to tackle viral-host interactions for the treatment of influenza virus infections. Eur J Pharmacol 2017; 809:178-190. [DOI: 10.1016/j.ejphar.2017.05.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/24/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022]
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26
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Chutiwitoonchai N, Mano T, Kakisaka M, Sato H, Kondoh Y, Osada H, Kotani O, Yokoyama M, Sato H, Aida Y. Inhibition of CRM1-mediated nuclear export of influenza A nucleoprotein and nuclear export protein as a novel target for antiviral drug development. Virology 2017; 507:32-39. [PMID: 28399435 PMCID: PMC7111614 DOI: 10.1016/j.virol.2017.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 12/18/2022]
Abstract
An anti-influenza compound, DP2392-E10 based on inhibition of the nuclear export function of the viral nucleoprotein-nuclear export signal 3 (NP-NES3) domain was successfully identified by our previous high-throughput screening system. Here, we demonstrated that DP2392-E10 exerts its antiviral effect by inhibiting replication of a broad range of influenza A subtypes. In regard to the molecular mechanism, we revealed that DP2392-E10 inhibits nuclear export of both viral NP and nuclear export protein (NEP). More specifically, in vitro pull-down assays revealed that DP2392-E10 directly binds cellular CRM1, which mediates nuclear export of NP and NEP. In silico docking suggested that DP2392-E10 binds at a region close to the HEAT9 and HEAT10 domains of CRM1. Together, these results indicate that the CRM1-mediated nuclear export function of influenza virus represents a new potential target for antiviral drug development, and also provide a core structure for a novel class of inhibitors that target this function.
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Affiliation(s)
| | - Takafumi Mano
- Viral Infectious Disease Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Michinori Kakisaka
- Viral Infectious Disease Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hirotaka Sato
- Viral Infectious Disease Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Osamu Kotani
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Yoko Aida
- Viral Infectious Disease Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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27
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Li R, Liu T, Liu M, Chen F, Liu S, Yang J. Anti-influenza A Virus Activity of Dendrobine and Its Mechanism of Action. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3665-3674. [PMID: 28417634 DOI: 10.1021/acs.jafc.7b00276] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Dendrobine, a major component of Dendrobium nobile, increasingly draws attention for its wide applications in health care. Here we explore potential effects of dendrobine against influenza A virus and elucidate the underlying mechanism. Our results indicated that dendrobine possessed antiviral activity against influenza A viruses, including A/FM-1/1/47 (H1N1), A/Puerto Rico/8/34 H274Y (H1N1), and A/Aichi/2/68 (H3N2) with IC50 values of 3.39 ± 0.32, 2.16 ± 0.91, 5.32 ± 1.68 μg/mL, respectively. Mechanism studies revealed that dendrobine inhibited early steps in the viral replication cycle. Notably, dendrobine could bind to the highly conserved region of viral nucleoprotein (NP), subsequently restraining nuclear export of viral NP and its oligomerization. In conclusion, dendrobine shows potential to be developed as a promising agent to treat influenza virus infection. More importantly, the results provide invaluable information for the full application of the Traditional Chinese Medicine named "Shi Hu".
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Affiliation(s)
- Richan Li
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, China
| | - Teng Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, China
| | - Miaomiao Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, China
| | - Feimin Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, China
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, China
| | - Jie Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, Guangzhou Key laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou 510515, China
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28
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Makau JN, Watanabe K, Ishikawa T, Mizuta S, Hamada T, Kobayashi N, Nishida N. Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approaches. PLoS One 2017; 12:e0173582. [PMID: 28273150 PMCID: PMC5342234 DOI: 10.1371/journal.pone.0173582] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/22/2017] [Indexed: 01/23/2023] Open
Abstract
Influenza viruses have acquired resistance to approved neuraminidase-targeting drugs, increasing the need for new drug targets for the development of novel anti-influenza drugs. Nucleoprotein (NP) is an attractive target since it has an indispensable role in virus replication and its amino acid sequence is well conserved. In this study, we aimed to identify new inhibitors of the NP using a structure-based drug discovery algorithm, named Nagasaki University Docking Engine (NUDE), which has been established especially for the Destination for GPU Intensive Machine (DEGIMA) supercomputer. The hit compounds that showed high binding scores during in silico screening were subsequently evaluated for anti-influenza virus effects using a cell-based assay. A 4-hydroxyquinolinone compound, designated as NUD-1, was found to inhibit the replication of influenza virus in cultured cells. Analysis of binding between NUD-1 and NP using surface plasmon resonance assay and fragment molecular orbital calculations confirmed that NUD-1 binds to NP and could interfere with NP-NP interactions essential for virus replication. Time-of-addition experiments showed that the compound inhibited the mid-stage of infection, corresponding to assembly of the NP and other viral proteins. Moreover, NUD-1 was also effective against various types of influenza A viruses including a clinical isolate of A(H1N1)pdm09 influenza with a 50% inhibitory concentration range of 1.8-2.1 μM. Our data demonstrate that the combined use of NUDE system followed by the cell-based assay is useful to obtain lead compounds for the development of novel anti-influenza drugs.
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Affiliation(s)
- Juliann Nzembi Makau
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
- Leading Program, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Ken Watanabe
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Satoshi Mizuta
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Tsuyoshi Hamada
- Nagasaki Advanced Computing Center, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Nobuyuki Kobayashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
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29
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Maeda N, Furukawa A, Kakita K, Anada M, Hashimoto S, Matsunaga S, Kuroki K, Ose T, Kato A, Arii J, Kawaguchi Y, Arase H, Maenaka K. Rapid Screening by Cell-Based Fusion Assay for Identifying Novel Antivirals of Glycoprotein B-Mediated Herpes Simplex Virus Type 1 Infection. Biol Pharm Bull 2017; 39:1897-1902. [PMID: 27803463 DOI: 10.1248/bpb.b16-00533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Herpes simplex virus type 1 (HSV-1) is a causative agent for a variety of diseases. Although antiherpetic drugs such as acyclovir have been developed to inhibit virus replication through interaction with DNA kinases, their continuous administration leads to an increase in the frequency of drug-resistant HSV-1, which is an important clinical issue that requires urgent solution. Recently, we reported that the sialylated O-linked sugar T antigen (sTn) and its attached peptide region (O-glycosylated sTn peptide) derived from the HSV-1 glycoprotein B (gB) protein inhibited HSV-1 infection by specifically targeting paired immunoglobulin-like type 2 receptor alpha (PILRα) in vitro. In this study, to further identify novel inhibitors of gB-mediated HSV-1 infection in vitro, we established a cell-based fusion assay for rapid drug screening. Chinese hamster ovary (CHO) cells were transfected with expression plasmids for HSV-1 gB, gD, gH, and gL, and T7 RNA polymerase, and were designated as the effector cells. The CHO-K1 cells stably expressing PILRα were transfected with the expression plasmid for firefly luciferase under the T7 promoter, and were designated as the target cells. The effector and target cells were co-cultured, and luminescence was measured when both cells were successfully fused. Importantly, we found that cell-to-cell fusion was specifically inhibited by O-glycosylated sTn peptide in a dose dependent manner. Our results suggested that this virus-free cell-based fusion assay system could be a useful and promising approach to identify novel inhibitors of gB-mediated HSV-1 infection, and will aid in the development of antiviral therapeutic strategies for HSV-1-associated diseases.
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Affiliation(s)
- Naoyoshi Maeda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University
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30
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Stevaert A, Naesens L. The Influenza Virus Polymerase Complex: An Update on Its Structure, Functions, and Significance for Antiviral Drug Design. Med Res Rev 2016; 36:1127-1173. [PMID: 27569399 PMCID: PMC5108440 DOI: 10.1002/med.21401] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/18/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
Influenza viruses cause seasonal epidemics and pandemic outbreaks associated with significant morbidity and mortality, and a huge cost. Since resistance to the existing anti‐influenza drugs is rising, innovative inhibitors with a different mode of action are urgently needed. The influenza polymerase complex is widely recognized as a key drug target, given its critical role in virus replication and high degree of conservation among influenza A (of human or zoonotic origin) and B viruses. We here review the major progress that has been made in recent years in unravelling the structure and functions of this protein complex, enabling structure‐aided drug design toward the core regions of the PA endonuclease, PB1 polymerase, or cap‐binding PB2 subunit. Alternatively, inhibitors may target a protein–protein interaction site, a cellular factor involved in viral RNA synthesis, the viral RNA itself, or the nucleoprotein component of the viral ribonucleoprotein. The latest advances made for these diverse pharmacological targets have yielded agents in advanced (i.e., favipiravir and VX‐787) or early clinical testing, besides several experimental inhibitors in various stages of development, which are all covered here.
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Affiliation(s)
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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31
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Naesens L, Stevaert A, Vanderlinden E. Antiviral therapies on the horizon for influenza. Curr Opin Pharmacol 2016; 30:106-115. [PMID: 27570127 DOI: 10.1016/j.coph.2016.08.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 01/12/2023]
Abstract
Adequate response to severe influenza infections or pandemic outbreaks requires two complementary strategies: preventive vaccination and antiviral therapy. The existing influenza drugs, M2 blockers and neuraminidase inhibitors, show modest clinical efficacy and established or potential resistance. In the past three years, several new agents have entered the clinical pipeline and already yielded some promising data from Phase 2 trials. For two main categories, that is, the broadly neutralizing anti-hemagglutinin antibodies and small-molecule inhibitors of the viral polymerase complex, crystallography was instrumental to guide drug development. These structural insights also aid to expand the activity spectrum towards influenza A plus B viruses, or conceive nucleoprotein or polymerase assembly inhibitors. The practice of influenza therapy should radically change in the next decade.
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Affiliation(s)
- Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Annelies Stevaert
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
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32
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Chutiwitoonchai N, Aida Y. NXT1, a Novel Influenza A NP Binding Protein, Promotes the Nuclear Export of NP via a CRM1-Dependent Pathway. Viruses 2016; 8:E209. [PMID: 27483302 PMCID: PMC4997571 DOI: 10.3390/v8080209] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 12/31/2022] Open
Abstract
Influenza remains a serious worldwide public health problem. After infection, viral genomic RNA is replicated in the nucleus and packed into viral ribonucleoprotein, which will then be exported to the cytoplasm via a cellular chromosome region maintenance 1 (CRM1)-dependent pathway for further assembly and budding. However, the nuclear export mechanism of influenza virus remains controversial. Here, we identify cellular nuclear transport factor 2 (NTF2)-like export protein 1 (NXT1) as a novel binding partner of nucleoprotein (NP) that stimulates NP-mediated nuclear export via the CRM1-dependent pathway. NXT1-knockdown cells exhibit decreased viral replication kinetics and nuclear accumulated viral RNA and NP. By contrast, NXT1 overexpression promotes nuclear export of NP in a CRM1-dependent manner. Pull-down assays suggest the formation of an NXT1, NP, and CRM1 complex, and demonstrate that NXT1 binds to the C-terminal region of NP. These findings reveal a distinct mechanism for nuclear export of the influenza virus and identify the NXT1/NP interaction as a potential target for antiviral drug development.
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Affiliation(s)
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, Wako, Saitama 351-0198, Japan.
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33
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Novel Chemical Ligands to Ebola Virus and Marburg Virus Nucleoproteins Identified by Combining Affinity Mass Spectrometry and Metabolomics Approaches. Sci Rep 2016; 6:29680. [PMID: 27403722 PMCID: PMC4940736 DOI: 10.1038/srep29680] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/20/2016] [Indexed: 12/25/2022] Open
Abstract
The nucleoprotein (NP) of Ebola virus (EBOV) and Marburg virus (MARV) is an essential component of the viral ribonucleoprotein complex and significantly impacts replication and transcription of the viral RNA genome. Although NP is regarded as a promising antiviral druggable target, no chemical ligands have been reported to interact with EBOV NP or MARV NP. We identified two compounds from a traditional Chinese medicine Gancao (licorice root) that can bind both NPs by combining affinity mass spectrometry and metabolomics approaches. These two ligands, 18β-glycyrrhetinic acid and licochalcone A, were verified by defined compound mixture screens and further characterized with individual ligand binding assays. Accompanying biophysical analyses demonstrate that binding of 18β-glycyrrhetinic acid to EBOV NP significantly reduces protein thermal stability, induces formation of large NP oligomers, and disrupts the critical association of viral ssRNA with NP complexes whereas the compound showed no such activity on MARV NP. Our study has revealed the substantial potential of new analytical techniques in ligand discovery from natural herb resources. In addition, identification of a chemical ligand that influences the oligomeric state and RNA-binding function of EBOV NP sheds new light on antiviral drug development.
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34
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Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2. Virology 2016; 496:116-126. [PMID: 27289560 DOI: 10.1016/j.virol.2016.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
To be incorporated into progeny virions, the viral genome must be transported to the inner leaflet of the plasma membrane (PM) and accumulate there. Some viruses utilize lipid components to assemble at the PM. For example, simian virus 40 (SV40) targets the ganglioside GM1 and human immunodeficiency virus type 1 (HIV-1) utilizes phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2]. Recent studies clearly indicate that Rab11-mediated recycling endosomes are required for influenza A virus (IAV) trafficking of vRNPs to the PM but it remains unclear how IAV vRNP localized or accumulate underneath the PM for viral genome incorporation into progeny virions. In this study, we found that the second intrinsically disordered region (IDR2) of NP regulates two binding steps involved in viral genome packaging. First, IDR2 facilitates NP oligomer binding to viral RNA to form vRNP. Secondly, vRNP assemble by interacting with PI(4,5)P2 at the PM via IDR2. These findings suggest that PI(4,5)P2 functions as the determinant of vRNP accumulation at the PM.
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35
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Recent discoveries of influenza A drug target sites to combat virus replication. Biochem Soc Trans 2016; 44:932-6. [DOI: 10.1042/bst20160002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 11/17/2022]
Abstract
Sequence variations in the binding sites of influenza A proteins are known to limit the effectiveness of current antiviral drugs. Clinically, this leads to increased rates of virus transmission and pathogenicity. Potential influenza A inhibitors are continually being discovered as a result of high-throughput cell based screening studies, whereas the application of computational tools to aid drug discovery has further increased the number of predicted inhibitors reported. This review brings together the aspects that relate to the identification of influenza A drug target sites and the findings from recent antiviral drug discovery strategies.
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36
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Yen HL. Current and novel antiviral strategies for influenza infection. Curr Opin Virol 2016; 18:126-34. [DOI: 10.1016/j.coviro.2016.05.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/15/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
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37
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Ehrt C, Brinkjost T, Koch O. Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design. J Med Chem 2016; 59:4121-51. [PMID: 27046190 DOI: 10.1021/acs.jmedchem.6b00078] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Modern rational drug design not only deals with the search for ligands binding to interesting and promising validated targets but also aims to identify the function and ligands of yet uncharacterized proteins having impact on different diseases. Additionally, it contributes to the design of inhibitors with distinct selectivity patterns and the prediction of possible off-target effects. The identification of similarities between binding sites of various proteins is a useful approach to cope with those challenges. The main scope of this perspective is to describe applications of different protein binding site comparison approaches to outline their applicability and impact on molecular design. The article deals with various substantial application domains and provides some outstanding examples to show how various binding site comparison methods can be applied to promote in silico drug design workflows. In addition, we will also briefly introduce the fundamental principles of different protein binding site comparison methods.
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Affiliation(s)
- Christiane Ehrt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Tobias Brinkjost
- Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, 44227 Dortmund, Germany.,Department of Computer Science, TU Dortmund University , Otto-Hahn-Straße 14, 44224 Dortmund, Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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38
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A high-throughput screening system targeting the nuclear export pathway via the third nuclear export signal of influenza A virus nucleoprotein. Virus Res 2016; 217:23-31. [PMID: 26948263 DOI: 10.1016/j.virusres.2016.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/07/2016] [Indexed: 11/22/2022]
Abstract
Two classes of antiviral drugs, M2 channel inhibitors and neuraminidase (NA) inhibitors, are currently approved for the treatment of influenza; however, the development of resistance against these agents limits their efficacy. Therefore, the identification of new targets and the development of new antiviral drugs against influenza are urgently needed. The third nuclear export signal (NES3) of nucleoprotein (NP) is the most important for viral replication among seven NESs encoded by four viral proteins, NP, M1, NS1, and NS2. NP-NES3 is critical for the nuclear export of NP, and targeting NP-NES3 is therefore a promising strategy that may lead to the development of antiviral drugs. However, a high-throughput screening (HTS) system to identify inhibitors of NP nuclear export has not been established. Here, we developed a novel HTS system to evaluate the inhibitory effects of compounds on the nuclear export pathway mediated by NP-NES3 using a MDCK cell line stably expressing NP-NES3 fused to a green fluorescent protein from aequorea coerulescens (AcGFP-NP-NES3) and a cell imaging analyzer. This HTS system was used to screen a 9600-compound library, leading to the identification of several hit compounds with inhibitory activity against the nuclear export of AcGFP-NP-NES3. The present HTS system provides a useful strategy for the identification of inhibitors targeting the nuclear export of NP via its NES3 sequence.
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Kanoh N. Photo-cross-linked small-molecule affinity matrix as a tool for target identification of bioactive small molecules. Nat Prod Rep 2016; 33:709-18. [DOI: 10.1039/c5np00117j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review describes the status of the photo-cross-linked small-molecule affinity matrix while providing a useful tutorial for academic and industrial chemical biologists who are involved or interested in drug target identification.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
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