1
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Liu J, Niu J, Xu L, Zhao H. Identification of Novel Neuraminidase Inhibitors as Potential Anti-Influenza Agents: Virtual Screening, Molecular Docking, in vitro Validation and Molecular Dynamic Simulation Studies. Cell Biochem Biophys 2025:10.1007/s12013-025-01734-1. [PMID: 40146495 DOI: 10.1007/s12013-025-01734-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2025] [Indexed: 03/29/2025]
Abstract
The influenza virus causes approximately hundreds of thousands of deaths annually. Coupled with the emergence of drug resistance, there is an urgent need to develop new drugs for the treatment of influenza. Neuraminidase (NA) has long been recognized as a valid drug target for anti-influenza therapy. Herein, in order to identify potential NA inhibitors with novel structures, we employed a structure-based virtual screening strategy to screen a library containing 1.6 million compounds. Based on XP docking score and free energy calculation results, the three compounds E570-1769, K788-4718, and C071-0424 were selected that may have better binding affinity for the NA protein compared to oseltamivir. Amongst, E570-1769 was identified to be the most potential hit. Docking study showed that E570-1769 bound to NA with a binding energy of -10.3 kcal/mol. Moreover, in silico ADME/T studies demonstrated the druggability of E570-1769 was quite well. Furthermore, in vitro assay demonstrated that E570-1769 inhibited the wild-type and H274Y-muatated NAs with IC50 values of 72.6 μM and 229 μM, respectively. Additionally, molecular dynamic (MD) simulation studies were performed to gain a deep insight into the binding modes of E570-1769 in complex with NA. While less potent than oseltamivir, the novel structure of E570-1769 and promising ADME/T properties indicates it as a promising lead for future research.
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Affiliation(s)
- Junya Liu
- Office of Drug Clinical Trials, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinbo Niu
- Office of Drug Clinical Trials, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lihua Xu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.
| | - Huiru Zhao
- Infectious Diseases Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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2
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Sabt A, Khaleel EF, Shaldam MA, Ebaid MS, Mustafa Badi R, Allayeh AK, Eldehna WM, Dziadek J. Discovery of new quinoline derivatives bearing 1-aryl-1,2,3-triazole motif as influenza H1N1 virus neuraminidase inhibitors. Bioorg Chem 2024; 151:107703. [PMID: 39137601 DOI: 10.1016/j.bioorg.2024.107703] [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: 06/11/2024] [Revised: 07/27/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
Sporadically and periodically, influenza outbreaks threaten global health and the economy. Antigen drift-induced influenza virus mutations hamper antiviral drug development. Thus, a novel antiviral agent is urgently needed to address medication inefficacy issues. Herein, sixteen new quinoline-triazole hybrids 6a-h and 9a-h were prepared and evaluated in vitro against the H1N1 virus. In particular, 6d, 6e, and 9b showed promising H1N1 antiviral activity with selective index (SI) CC50/IC50 values of 15.8, 37, and 29.15. After that, the inhibition rates for various mechanisms of action (virus replication, adsorption, and virucidal activity) were investigated for the most efficient candidates 6d, 6e, and 9b. Additionally, their ability to inhibit neuraminidase was evaluated. With an IC50 value of 0.30 µM, hybrid 6d demonstrated effective and comparable inhibitory activity to Oseltamivir. Ultimately, molecular modeling investigations, encompassing molecular docking and molecular dynamic simulations, were conducted to provide a scientific basis for the observed antiviral results.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Cairo 12622, Egypt.
| | - Eman F Khaleel
- Department of Medical Physiology, College of Medicine, King Khalid University, Asir 61421, Saudi Arabia
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Manal S Ebaid
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Cairo 12622, Egypt; Department of Chemistry, College of Science, Northern Border University, Arar, Saudi Arabia
| | - Rehab Mustafa Badi
- Department of Medical Physiology, College of Medicine, King Khalid University, Asir 61421, Saudi Arabia
| | - Abdou K Allayeh
- Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University in Alexandria, Canal El Mahmoudia St., Alexandria 21648, Egypt.
| | - Jaroslaw Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
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3
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Fu SK, Cheng LP. Discovery andsynthesis of novel benzoylhydrazone neuraminidase inhibitors. Bioorg Med Chem Lett 2024; 105:129743. [PMID: 38608962 DOI: 10.1016/j.bmcl.2024.129743] [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: 02/06/2024] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/14/2024]
Abstract
Neuraminidase (NA) serves as a promising target for the exploration and development of anti-influenza drugs. In this work, lead compound 5 was discovered through pharmacophore-based virtual screening and molecular dynamics simulation, and 14 new compounds were obtained by modifying the lead compound 5 based on pharmacophore features. The biological activity test shows that 5n (IC50 = 0.13 μM) has a better inhibitory effect on wild-type NA (H5N1), while 5i (IC50 = 0.44 μM) has a prominent inhibitory effect on mutant NA (H5N1-H274Y), both of them are better than the positive control oseltamivir carboxylate (OSC). The analysis of docking results indicate that the good activities of compounds 5n and 5i may be attributed to the thiophene ring in 5n can stretch into the 150-cavity of NA, whereas the thiophene moiety in 5i can extend to the 430-cavity of NA. The findings of this study may be helpful for the discovery of new NA inhibitors.
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Affiliation(s)
- Shi Kai Fu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Li Ping Cheng
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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4
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Zhang J, Liu C, Jia R, Zhang X, Zhang J, Bertagnin C, Bonomini A, Guizzo L, Jiang Y, Jia H, Jia S, Ma X, Loregian A, Huang B, Zhan P, Liu X. A novel N-heterocycles substituted oseltamivir derivatives as potent inhibitors of influenza virus neuraminidase: discovery, synthesis and biological evaluation. J Enzyme Inhib Med Chem 2023; 38:2277135. [PMID: 37955306 PMCID: PMC10653643 DOI: 10.1080/14756366.2023.2277135] [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: 04/21/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
Our previous studies have shown that the introduction of structurally diverse benzyl side chains at the C5-NH2 position of oseltamivir to occupy 150-cavity contributes to the binding affinity with neuraminidase and anti-influenza activity. To obtain broad-spectrum neuraminidase inhibitors, we designed and synthesised a series of novel oseltamivir derivatives bearing different N-heterocycles substituents that have been proved to induce opening of the 150-loop of group-2 neuraminidases. Among them, compound 6k bearing 4-((r)-2-methylpyrrolidin-1-yl) benzyl group exhibited antiviral activities similar to or weaker than those of oseltamivir carboxylate against H1N1, H3N2, H5N1, H5N6 and H5N1-H274Y mutant neuraminidases. More encouragingly, 6k displayed nearly 3-fold activity enhancement against H3N2 virus over oseltamivir carboxylate and 2-fold activity enhancement over zanamivir. Molecular docking studies provided insights into the explanation of its broad-spectrum potency against wild-type neuraminidases. Overall, as a promising lead compound, 6k deserves further optimisation by fully considering the ligand induced flexibility of the 150-loop.
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Affiliation(s)
- Jiwei Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
- Suzhou Research Institute of Shandong University, Suzhou, Jiangsu, P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Jian Zhang
- Institute of Medical Sciences, The Second Hospital, Shandong University, Jinan, Shandong, P.R. China
| | - Chiara Bertagnin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Anna Bonomini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Laura Guizzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Yuanmin Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Huinan Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Shuzhen Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, Shandong, P.R. China
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 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, Jinan, Shandong, P.R. China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, PR 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, Jinan, Shandong, P.R. China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Jinan, Shandong, PR China
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5
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Gao R, Pascua PNQ, Nguyen HT, Chesnokov A, Champion C, Mishin VP, Wentworth DE, Gubareva LV. New insights into the neuraminidase-mediated hemagglutination activity of influenza A(H3N2) viruses. Antiviral Res 2023; 218:105719. [PMID: 37717821 PMCID: PMC10549826 DOI: 10.1016/j.antiviral.2023.105719] [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: 07/17/2023] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
Influenza virus neuraminidase (NA) can act as a receptor-binding protein, a role commonly attributed to hemagglutinin (HA). In influenza A(H3N2) viruses, three NA amino acid residues have previously been associated with NA-mediated hemagglutination: T148, D151, and more recently, H150. These residues are part of the 150-loop of the NA monomer. Substitutions at 148 and 151 arise from virus propagation in laboratory cell cultures, whereas changes at 150 occurred during virus evolution in the human host. In this study, we examined the effect of natural amino acid polymorphism at position 150 on NA-mediated hemagglutination. Using the A/Puerto Rico/8/34 backbone, we generated a comprehensive panel of recombinant A(H3N2) viruses that have different NAs but shared an HA that displays poor binding to red blood cells (RBCs). None of the tested substitutions at 150 (C, H, L, R, and S) promoted NA-binding. However, we identified two new determinants of NA-binding, Q136K and T439R, that emerged during virus culturing. Similar to T148I, both Q136K and T439R reduced NA enzyme activity by 48-86% and inhibition (14- to 173-fold) by the NA inhibitor zanamivir. NA-binding was observed when a virus preparation contained approximately 10% of NA variants with either T148I or T439R, highlighting the benefit of using deep sequencing in virus characterization. Taken together, our findings provide new insights into the molecular mechanisms underlying the ability of NA to function as a binding protein. Information gained may aid in the design of new and improved NA-targeting antivirals.
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Affiliation(s)
- Rongyuan Gao
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | | | - Ha T Nguyen
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Anton Chesnokov
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Chloe Champion
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA; Chippewa Government Solutions, Sault Sainte Marie, MI, USA
| | - Vasiliy P Mishin
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Dave E Wentworth
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Larisa V Gubareva
- Influenza Division, NCIRD, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA.
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6
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Yu X, Zhao X, Zhang Q, Dai C, Huang Q, Zhang L, Liu Y, Shen Y, Lin Z. Discovery of Neuraminidase Inhibitors based on 3D‐QSAR, Molecular Docking and MD Simulations. ChemistrySelect 2023. [DOI: 10.1002/slct.202203978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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7
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Discovery of N-substituted oseltamivir derivatives as novel neuraminidase inhibitors with improved drug resistance profiles and favorable drug-like properties. Eur J Med Chem 2023; 252:115275. [PMID: 36931117 DOI: 10.1016/j.ejmech.2023.115275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/25/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023]
Abstract
To yield potent neuraminidase inhibitors with improved drug resistance and favorable drug-like properties, two series of novel oseltamivir derivatives targeting the 150-cavity of neuraminidase were designed, synthesized, and biologically evaluated. Among the synthesized compounds, the most potent compound 43b bearing 3-floro-4-cyclopentenylphenzyl moiety exhibited weaker or slightly improved inhibitory activity against wild-type neuraminidases (NAs) of H1N1, H5N1, and H5N8 compared to oseltamivir carboxylate (OSC). Encouragingly, 43b displayed 62.70- and 5.03-fold more potent activity than OSC against mutant NAs of H5N1-H274Y and H1N1-H274Y, respectively. In cellular antiviral assays, 43b exerted equivalent or more potent activities against H1N1, H5N1, and H5N8 compared to OSC with no significant cytotoxicity up to 200 μM. Notably, 43b displayed potent antiviral efficacy in the embryonated egg model, in which achieved a protective effect against H5N1 and H5N8 similar to OSC. Molecular docking studies were implemented to reveal the binding mode of 43b in the binding pocket. Moreover, 43b possessed improved physicochemical properties and ADMET properties compared to OSC by in silico prediction. Taken together, 43b appeared to be a promising lead compound for further investigation.
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8
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Klenow L, Elfageih R, Gao J, Wan H, Withers SG, de Gier JW, Daniels R. Influenza virus and pneumococcal neuraminidases enhance catalysis by similar yet distinct sialic acid-binding strategies. J Biol Chem 2023; 299:102891. [PMID: 36634846 PMCID: PMC9929470 DOI: 10.1016/j.jbc.2023.102891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Influenza A viruses and the bacterium Streptococcus pneumoniae (pneumococci) both express neuraminidases that catalyze release of sialic acid residues from oligosaccharides and glycoproteins. Although these respiratory pathogen neuraminidases function in a similar environment, it remains unclear if these enzymes use similar mechanisms for sialic acid cleavage. Here, we compared the enzymatic properties of neuraminidases from two influenza A subtypes (N1 and N2) and the pneumococcal strain TIGR4 (NanA, NanB, and NanC). Insect cell-produced N1 and N2 tetramers exhibited calcium-dependent activities and stabilities that varied with pH. In contrast, E. coli-produced NanA, NanB, and NanC were isolated as calcium insensitive monomers with stabilities that were more resistant to pH changes. Using a synthetic substrate (MUNANA), all neuraminidases showed similar pH optimums (pH 6-7) that were primarily defined by changes in catalytic rate rather than substrate binding affinity. Upon using a multivalent substrate (fetuin sialoglycans), much higher specific activities were observed for pneumococcal neuraminidases that contain an additional lectin domain. In virions, N1 and especially N2 also showed enhanced specific activity toward fetuin that was lost upon the addition of detergent, indicating the sialic acid-binding capacity of neighboring hemagglutinin molecules likely contributes to catalysis of natural multivalent substrates. These results demonstrate that influenza and pneumococcal neuraminidases have evolved similar yet distinct strategies to optimize their catalytic activity.
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Affiliation(s)
- Laura Klenow
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Rageia Elfageih
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jin Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Robert Daniels
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA.
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9
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Structural and inhibitor sensitivity analysis of influenza B-like viral neuraminidases derived from Asiatic toad and spiny eel. Proc Natl Acad Sci U S A 2022; 119:e2210724119. [PMID: 36191180 PMCID: PMC9586306 DOI: 10.1073/pnas.2210724119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza virus neuraminidase (NA) is an important target for antiviral development because it plays a crucial role in releasing newly assembled viruses. Two unique influenza-like virus genomes were recently reported in the Wuhan Asiatic toad and Wuhan spiny eel. Their NA genes appear to be highly divergent from all known influenza NAs, raising key questions as to whether the Asiatic toad influenza-like virus NA (tNA) and spiny eel NA (eNA) have canonical NA activities and structures and whether they show sensitivity to NA inhibitors (NAIs). Here, we found that both tNA and eNA have neuraminidase activities. A detailed structural analysis revealed that tNA and eNA present similar overall structures to currently known NAs, with a conserved calcium binding site. Inhibition assays indicated that tNA is resistant to NAIs, while eNA is still sensitive to NAIs. E119 is conserved in canonical NAs. The P119E substitution in tNA can restore sensitivity to NAIs, and, in contrast, the E119P substitution in eNA decreased its sensitivity to NAIs. The structures of NA-inhibitor complexes further provide a detailed insight into NA-inhibitor interactions at the atomic level. Moreover, tNA and eNA have unique N-glycosylation sites compared with canonical NAs. Collectively, the structural features, NA activities, and sensitivities to NAIs suggest that fish- and amphibian-derived influenza-like viruses may circulate in these vertebrates. More attention should be paid to these influenza-like viruses because their NA molecules may play roles in the emergence of NAI resistance.
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10
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Jia R, Zhang J, Zhang J, Bertagnin C, Bonomini A, Guizzo L, Gao Z, Ji X, Li Z, Liu C, Ju H, Ma X, Loregian A, Huang B, Zhan P, Liu X. Discovery of Novel Boron-Containing N-Substituted Oseltamivir Derivatives as Anti-Influenza A Virus Agents for Overcoming N1-H274Y Oseltamivir-Resistant. Molecules 2022; 27:molecules27196426. [PMID: 36234966 PMCID: PMC9571049 DOI: 10.3390/molecules27196426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022] Open
Abstract
To address drug resistance to influenza virus neuraminidase inhibitors (NAIs), a series of novel boron-containing N-substituted oseltamivir derivatives were designed and synthesized to target the 150-cavity of neuraminidase (NA). In NA inhibitory assays, it was found that most of the new compounds exhibited moderate inhibitory potency against the wild-type NAs. Among them, compound 2c bearing 4-(3-boronic acid benzyloxy)benzyl group displayed weaker or slightly improved activities against group-1 NAs (H1N1, H5N1, H5N8 and H5N1-H274Y) compared to that of oseltamivir carboxylate (OSC). Encouragingly, 2c showed 4.6 times greater activity than OSC toward H5N1-H274Y NA. Moreover, 2c exerted equivalent or more potent antiviral activities than OSC against H1N1, H5N1 and H5N8. Additionally, 2c demonstrated low cytotoxicity in vitro and no acute toxicity at the dose of 1000 mg/kg in mice. Molecular docking of 2c was employed to provide a possible explanation for the improved anti-H274Y NA activity, which may be due to the formation of key additional hydrogen bonds with surrounding amino acid residues, such as Arg152, Gln136 and Val149. Taken together, 2c appeared to be a promising lead compound for further optimization.
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Affiliation(s)
- Ruifang Jia
- 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 250012, China
| | - Jiwei Zhang
- 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 250012, China
| | - Jian Zhang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, China
| | - Chiara Bertagnin
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Anna Bonomini
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Laura Guizzo
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Zhen Gao
- 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 250012, China
| | - Xiangkai Ji
- 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 250012, China
| | - Zhuo Li
- 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 250012, China
| | - Chuanfeng 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 250012, China
| | - Han Ju
- 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 250012, China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 1 Jiaoxiao Road, Jinan 250023, China
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 1 Jiaoxiao Road, Jinan 250023, China
- Correspondence: (B.H.); (P.Z.); (X.L.)
| | - 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 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (B.H.); (P.Z.); (X.L.)
| | - 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 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (B.H.); (P.Z.); (X.L.)
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11
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Ju H, Hou L, Zhao F, Zhang Y, Jia R, Guizzo L, Bonomini A, Zhang J, Gao Z, Liang R, Bertagnin C, Kong X, Ma X, Kang D, Loregian A, Huang B, Liu X, Zhan P. Iterative Optimization and Structure-Activity Relationship Studies of Oseltamivir Amino Derivatives as Potent and Selective Neuraminidase Inhibitors via Targeting 150-Cavity. J Med Chem 2022; 65:11550-11573. [PMID: 35939763 DOI: 10.1021/acs.jmedchem.1c01970] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With our continuous endeavors in seeking neuraminidase (NA) inhibitors, we reported herein three series of novel oseltamivir amino derivatives with the goal of exploring the druggable chemical space inside the 150-cavity of influenza virus NAs. Among them, around half of the compounds in series C were demonstrated to be better inhibitors against both wild-type and oseltamivir-resistant group-1 NAs than oseltamivir carboxylate (OSC). Notably, compounds 12d, 12e, 15e, and 15i showed more potent or equipotent antiviral activity against H1N1, H5N1, and H5N8 viruses compared to OSC in cellular assays. Furthermore, compounds 12e and 15e exhibited high metabolic stability in human liver microsomes (HLMs) and low inhibitory effect on main cytochrome P450 (CYP) enzymes, as well as low acute/subacute toxicity and certain antiviral efficacy in vivo. Also, pharmacokinetic (PK) and molecular docking studies were performed. Overall, 12e and 15e possess great potential to serve as anti-influenza candidates and are worthy of further investigation.
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Affiliation(s)
- Han Ju
- 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, 250012 Jinan, Shandong, P. R. China
| | - Lingxin Hou
- 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, 250012 Jinan, Shandong, P. R. China
| | - Fabao Zhao
- 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, 250012 Jinan, Shandong, P. R. China
| | - Ying Zhang
- 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, 250012 Jinan, Shandong, P. R. China
| | - Ruifang Jia
- 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, 250012 Jinan, Shandong, P. R. China
| | - Laura Guizzo
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Anna Bonomini
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Jiwei Zhang
- 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, 250012 Jinan, Shandong, P. R. China
| | - Zhen Gao
- 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, 250012 Jinan, Shandong, P. R. China
| | - Ruipeng Liang
- 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, 250012 Jinan, Shandong, P. R. China
| | - Chiara Bertagnin
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Xiujie Kong
- 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, 250012 Jinan, Shandong, P. R. China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 202 North Gongye Road, 250100 Jinan, Shandong, P. R. China
| | - Dongwei Kang
- 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, 250012 Jinan, Shandong, P. R. China
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 202 North Gongye Road, 250100 Jinan, Shandong, 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, 250012 Jinan, Shandong, 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, 250012 Jinan, Shandong, P. R. China
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12
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Abstract
The continuous emergence and reemergence of diverse subtypes of influenza A viruses, which are known as "HxNy" and are mediated through the reassortment of viral genomes, account for seasonal epidemics, occasional pandemics, and zoonotic outbreaks. We summarize and discuss the characteristics of historic human pandemic HxNy viruses and diverse subtypes of HxNy among wild birds, mammals, and live poultry markets. In addition, we summarize the key molecular features of emerging infectious HxNy influenza viruses from the perspectives of the receptor binding of Hx, the inhibitor-binding specificities and drug-resistance features of Ny, and the matching of the gene segments. Our work enhances our understanding of the potential threats of novel reassortant influenza viruses to public health and provides recommendations for effective prevention, control, and research of this pathogen.
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Affiliation(s)
- William J Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Yan Wu
- Department of Pathogen Microbiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Weifeng Shi
- Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an 271016, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences (CAS), Beijing 100101, China
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13
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Design, synthesis and biological evaluation of 1,3,4-triazole-3-acetamide derivatives as potent neuraminidase inhibitors. Bioorg Med Chem Lett 2022; 61:128590. [DOI: 10.1016/j.bmcl.2022.128590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 01/07/2023]
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14
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Abstract
Depending on the strain, influenza A virus causes animal, zoonotic, pandemic, or seasonal influenza with varying degrees of severity. Two surface glycoprotein spikes, hemagglutinin (HA) and neuraminidase (NA), are the most important influenza A virus antigens. NA plays an important role in the propagation of influenza virus by removing terminal sialic acid from sialyl decoy receptors and thereby facilitating the release of viruses from traps such as in mucus and on infected cells. Some NA inhibitors have become widely used drugs for treatment of influenza. However, attempts to develop effective and safe NA inhibitors that can be used for treatment of anti-NA drugs-resistant influenza viruses have continued. In this chapter, we describe the following updates on influenza A NA inhibitor development: (i) N-acetylneuraminic acid (Neu5Ac)-based derivatives, (ii) covalent NA inhibitors, (iii) sulfo-sialic acid analogs, (iv) N-acetyl-6-sulfo-β-D-glucosaminide-based inhibitors, (v) inhibitors targeting the 150-loop of group 1 NAs, (vi) conjugation inhibitors, (vii) acylhydrazone derivatives, (viii) monoclonal antibodies, (ix) PVP-I, and (x) natural products. Finally, we provide future perspectives on the next-generation anti-NA drugs.
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Affiliation(s)
- Nongluk Sriwilaijaroen
- Department of Preclinical Sciences, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
- Department of Medical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | | | - Hiromasa Kiyota
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yasuo Suzuki
- Department of Medical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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15
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Sapachova M, Kovalenko G, Sushko M, Bezymennyi M, Muzyka D, Usachenko N, Mezhenskyi A, Abramov A, Essen S, Lewis NS, Bortz E. Phylogenetic Analysis of H5N8 Highly Pathogenic Avian Influenza Viruses in Ukraine, 2016–2017. Vector Borne Zoonotic Dis 2021; 21:979-988. [DOI: 10.1089/vbz.2021.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Maryna Sapachova
- State Scientific and Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise (SSRILDVSE), Kyiv, Ukraine
| | - Ganna Kovalenko
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Department of Biological Sciences, University of Alaska Anchorage (UAA), Anchorage, Alaska, USA
| | - Mykola Sushko
- State Scientific and Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise (SSRILDVSE), Kyiv, Ukraine
| | | | - Denys Muzyka
- National Scientific Center Institute for Experimental Clinical and Veterinary Medicine (NSC IECVM), Kharkiv, Ukraine
| | - Natalia Usachenko
- State Scientific and Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise (SSRILDVSE), Kyiv, Ukraine
| | - Andrii Mezhenskyi
- State Scientific and Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise (SSRILDVSE), Kyiv, Ukraine
| | - Artur Abramov
- State Scientific Control Institute of Biotechnology and Strains of Microorganisms (SSCIBSM), Kyiv, Ukraine
| | - Stephen Essen
- OIE/FAO International Reference Laboratory, Animal and Plant Health Agency (APHA), Weybridge, United Kingdom
| | - Nicola S. Lewis
- OIE/FAO International Reference Laboratory, Animal and Plant Health Agency (APHA), Weybridge, United Kingdom
- Royal Veterinary College, University of London, London, United Kingdom
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage (UAA), Anchorage, Alaska, USA
- Institute for Veterinary Medicine (IVM), Kyiv, Ukraine
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16
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Creytens S, Pascha MN, Ballegeer M, Saelens X, de Haan CAM. Influenza Neuraminidase Characteristics and Potential as a Vaccine Target. Front Immunol 2021; 12:786617. [PMID: 34868073 PMCID: PMC8635103 DOI: 10.3389/fimmu.2021.786617] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/29/2021] [Indexed: 12/28/2022] Open
Abstract
Neuraminidase of influenza A and B viruses plays a critical role in the virus life cycle and is an important target of the host immune system. Here, we highlight the current understanding of influenza neuraminidase structure, function, antigenicity, immunogenicity, and immune protective potential. Neuraminidase inhibiting antibodies have been recognized as correlates of protection against disease caused by natural or experimental influenza A virus infection in humans. In the past years, we have witnessed an increasing interest in the use of influenza neuraminidase to improve the protective potential of currently used influenza vaccines. A number of well-characterized influenza neuraminidase-specific monoclonal antibodies have been described recently, most of which can protect in experimental challenge models by inhibiting the neuraminidase activity or by Fc receptor-dependent mechanisms. The relative instability of the neuraminidase poses a challenge for protein-based antigen design. We critically review the different solutions that have been proposed to solve this problem, ranging from the inclusion of stabilizing heterologous tetramerizing zippers to the introduction of inter-protomer stabilizing mutations. Computationally engineered neuraminidase antigens have been generated that offer broad, within subtype protection in animal challenge models. We also provide an overview of modern vaccine technology platforms that are compatible with the induction of robust neuraminidase-specific immune responses. In the near future, we will likely see the implementation of influenza vaccines that confront the influenza virus with a double punch: targeting both the hemagglutinin and the neuraminidase.
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MESH Headings
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigenic Drift and Shift
- Antigens, Viral/immunology
- Antigens, Viral/ultrastructure
- Catalytic Domain/genetics
- Catalytic Domain/immunology
- Cross Protection
- Evolution, Molecular
- Humans
- Immunogenicity, Vaccine
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Alphainfluenzavirus/enzymology
- Alphainfluenzavirus/genetics
- Alphainfluenzavirus/immunology
- Betainfluenzavirus/enzymology
- Betainfluenzavirus/genetics
- Betainfluenzavirus/immunology
- Mutation
- Nanoparticles
- Neuraminidase/administration & dosage
- Neuraminidase/genetics
- Neuraminidase/immunology
- Neuraminidase/ultrastructure
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/ultrastructure
- Viral Proteins/administration & dosage
- Viral Proteins/genetics
- Viral Proteins/immunology
- Viral Proteins/ultrastructure
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Affiliation(s)
- Sarah Creytens
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Mirte N. Pascha
- Section Virology, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
| | - Marlies Ballegeer
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Cornelis A. M. de Haan
- Section Virology, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
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17
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Ye J, Lin L, Xu J, Chan PKS, Yang X, Ma C. Design, Synthesis, Biological Evaluation and In Silico Studies of Pyrazole-Based NH 2-Acyl Oseltamivir Analogues as Potent Neuraminidase Inhibitors. Pharmaceuticals (Basel) 2021; 14:371. [PMID: 33923858 PMCID: PMC8073777 DOI: 10.3390/ph14040371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Oseltamivir represents one of the most successful neuraminidase (NA) inhibitors in the current anti-influenza therapy. The 150-cavity of NA was identified as an additional binding pocket, and novel NA inhibitors have been designed to occupy the 150-cavity based on the structure information of oseltamivir carboxylate (OC) in complex with NA. In this study, a series of C-5-NH2-acyl derivatives of OC containing the pyrazole moiety were synthesized. Several derivatives exhibited substantial inhibitory activity against NA. Moreover, in silico ADME evaluation indicated that the derivatives were drug-like with higher oral absorption rates and greater cell permeability than OC. Additionally, molecular docking studies revealed that the derivatives interacted with both the NA enzyme active site and 150-cavity as expected. The results provided useful information for further structural optimization of OC.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China;
| | - Lin Lin
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China; (L.L.); (P.K.-s.C.)
| | - Jinyi Xu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, China;
| | - Paul Kay-sheung Chan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China; (L.L.); (P.K.-s.C.)
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China; (L.L.); (P.K.-s.C.)
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China;
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18
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Wang P, Oladejo BO, Li C, Fu L, Zhang S, Qi J, Lv X, Li X. Structure-based design of 5'-substituted 1,2,3-triazolylated oseltamivir derivatives as potent influenza neuraminidase inhibitors. RSC Adv 2021; 11:9528-9541. [PMID: 35423449 PMCID: PMC8696196 DOI: 10.1039/d1ra00472g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Resistant viruses containing mutant neuraminidases (NAs) with diminished drug affinity continue to emerge, and new anti-influenza agents are urgently required. Several potent inhibitors targeting the hydrophobic 150-cavity of viral NAs have been developed by modifying the antiviral drugs, oseltamivir carboxylate (OSC) and zanamivir, with hydrophobic groups. Here, we describe a different strategy for exploring novel and efficient NA inhibitors by targeting the charged amino acid residues around the entrance to the 150-cavity. We synthesized a C5-substituted OSC derivative (1e) with a 4'-phenyl-1,2,3-triazolyl group capable of entering the 150-cavity, and solved the crystal structure of 1e in complex with influenza A virus N5 NA. Using the resulting structural information, we next designed and synthesized two series of OSC derivatives carrying various polar substituents at the triazolyl group of 1e and 2e, with 2e being a 5'-phenyl-1,2,3-triazole regioisomer of 1e. The NA inhibition assays demonstrated that the 2 series (2e-n) generally had superior activity compared with the 1 series (1e-n). Compound 2j, bearing a 3-phenylamino group on the triazole ring, was the most potent inhibitor of all tested NAs including an N2 NA containing the E119V OSC-resistant mutation. Moreover, 2j potently inhibited viral replication in vitro, and molecular docking studies revealed that its phenylamino group can form an additional strong hydrogen bond with residue D151 near the entrance of the 150-cavity. The design method described in this study provides useful insights into the development of novel NA inhibitors. Compound 2j warrants further structural optimization to obtain a candidate for clinical use.
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Affiliation(s)
- Pengfei Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences Huairou District Beijing 101408 China
| | - Babayemi O Oladejo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
- Department of Microbiology, Federal University of Technology PMB 704 Akure Nigeria
| | - Chenning Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences Huairou District Beijing 101408 China
| | - Lifeng Fu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
- Center for Influenza Research and Early-warning, Chinese Academy of Sciences (CASCIRE) Chaoyang District Beijing 100101 China
| | - Shanshan Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences Huairou District Beijing 101408 China
| | - Xun Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences Huairou District Beijing 101408 China
- Center for Influenza Research and Early-warning, Chinese Academy of Sciences (CASCIRE) Chaoyang District Beijing 100101 China
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19
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Timonina D, Sharapova Y, Švedas V, Suplatov D. Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies. Comput Struct Biotechnol J 2021; 19:1302-1311. [PMID: 33738079 PMCID: PMC7933735 DOI: 10.1016/j.csbj.2021.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Local 3D-structural differences in homologous proteins contribute to functional diversity observed in a superfamily, but so far received little attention as bioinformatic analysis was usually carried out at the level of amino acid sequences. We have developed Zebra3D - the first-of-its-kind bioinformatic software for systematic analysis of 3D-alignments of protein families using machine learning. The new tool identifies subfamily-specific regions (SSRs) - patterns of local 3D-structure (i.e. single residues, loops, or secondary structure fragments) that are spatially equivalent within families/subfamilies, but are different among them, and thus can be associated with functional diversity and function-related conformational plasticity. Bioinformatic analysis of protein superfamilies by Zebra3D can be used to study 3D-determinants of catalytic activity and specific accommodation of ligands, help to prepare focused libraries for directed evolution or assist development of chimeric enzymes with novel properties by exchange of equivalent regions between homologs, and to characterize plasticity in binding sites. A companion Mustguseal web-server is available to automatically construct a 3D-alignment of functionally diverse proteins, thus reducing the minimal input required to operate Zebra3D to a single PDB code. The Zebra3D + Mustguseal combined approach provides the opportunity to systematically explore the value of SSRs in superfamilies and to use this information for protein design and drug discovery. The software is available open-access at https://biokinet.belozersky.msu.ru/Zebra3D.
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Affiliation(s)
- Daria Timonina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
| | - Yana Sharapova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Vytas Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1-73, Moscow 119234, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
| | - Dmitry Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1-73, Moscow 119234, Russia
- Corresponding author.
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20
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Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. mBio 2020; 11:mBio.02315-20. [PMID: 33024040 PMCID: PMC7542365 DOI: 10.1128/mbio.02315-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The immune system produces antibodies to protect the human body from harmful invaders. The monoclonal antibody (MAb) is one kind of effective antivirals. In this study, we isolated an antibody (Z2B3) from an H7N9 influenza virus-infected child. It shows cross-reactivity to both group 1 (N1) and group 2 (N9) neuraminidases (NAs) but is sensitive to N1 NA with a K432E substitution. Structural analysis of the NA-antibody fragment antigen-binding (Fab) complex provides a clue for antibody modification, and the modified antibody restored binding and inhibition to recently drifted N1 NA and regained protection against the variant influenza strain. This finding suggests that antibodies to NA may be a useful therapy and can be in principle edited to defeat drifted influenza virus. Here, we investigate a monoclonal antibody, Z2B3, isolated from an H7N9-infected patient, that exhibited cross-reactivity to both N9 (group 2) and a broad range of seasonal and avian N1 (group 1) proteins but lost activity to the N1 with the substitution K432E. This substitution exists in 99.25% of seasonal influenza strains after 2013. The NA-Z2B3 complex structures indicated that Z2B3 binds within the conserved active site of the neuraminidase (NA) protein. A salt bridge between D102 in Z2B3 and K432 in NA plays an important role in binding. Structure-based modification of Z2B3 with D102R in heavy chain reversed the salt bridge and restored the binding and inhibition of N1 with E432. Furthermore, Z2B3-D102R can protect mice from A/Serbia/NS-601/2014 H1N1 virus (NA contains E432) infection while the wild-type Z2B3 antibody shows no protection. This study demonstrates that a broadly reactive and protective antibody to NA can be in principle edited to restore binding and inhibition to recently drifted N1 NA and regain protection against the variant influenza strain.
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21
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Discovery of novel “Dual-site” binding oseltamivir derivatives as potent influenza virus neuraminidase inhibitors. Eur J Med Chem 2020; 191:112147. [DOI: 10.1016/j.ejmech.2020.112147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/25/2022]
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22
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Li P, Du R, Wang Y, Hou X, Wang L, Zhao X, Zhan P, Liu X, Rong L, Cui Q. Identification of Chebulinic Acid and Chebulagic Acid as Novel Influenza Viral Neuraminidase Inhibitors. Front Microbiol 2020; 11:182. [PMID: 32256457 PMCID: PMC7093024 DOI: 10.3389/fmicb.2020.00182] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022] Open
Abstract
The influenza A virus (IAV) causes seasonal epidemics and occasional but devastating pandemics, which are of a major public health concern. Although several antiviral drugs are currently available, there is an urgent need to develop novel antiviral therapies with different mechanisms of action due to emergence of drug resistance. In this study, two related compounds, chebulagic acid (CHLA) and chebulinic acid (CHLI), were identified as novel inhibitors against IAV replication. A reporter virus-based infection assay demonstrated that CHLA and CHLI exhibit no inhibitory effect on IAV entry or RNA replication during the virus replication cycle. Results of viral release inhibition assay and neuraminidase (NA) inhibition assay indicated that CHLA and CHLI exert their inhibitory effect on the NA-mediated viral release. Moreover, oseltamivir-resistance mutation NA/H274Y of NA is susceptible to CHLA or CHLI, suggesting a different mechanism of action for CHLA and CHLI. In summary, CHLA and CHLI are promising new NA inhibitors that may be further developed as novel antivirals against IAVs.
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Affiliation(s)
- Ping Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
- Research Center, College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yanyan Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xuewen Hou
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lin Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiujuan Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
- Research Center, College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
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23
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Deeks HM, Walters RK, Hare SR, O’Connor MB, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking. PLoS One 2020; 15:e0228461. [PMID: 32160194 PMCID: PMC7065745 DOI: 10.1371/journal.pone.0228461] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interactive molecular dynamics in virtual reality (iMD-VR) as an accurate low-cost strategy for flexible protein-ligand docking. We outline an experimental protocol which enables expert iMD-VR users to guide ligands into and out of the binding pockets of trypsin, neuraminidase, and HIV-1 protease, and recreate their respective crystallographic protein-ligand binding poses within 5-10 minutes. Following a brief training phase, our studies shown that iMD-VR novices were able to generate unbinding and rebinding pathways on similar timescales as iMD-VR experts, with the majority able to recover binding poses within 2.15 Å RMSD of the crystallographic binding pose. These results indicate that iMD-VR affords sufficient control for users to carry out the detailed atomic manipulations required to dock flexible ligands into dynamic enzyme active sites and recover crystallographic poses, offering an interesting new approach for simulating drug docking and generating binding hypotheses.
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Affiliation(s)
- Helen M. Deeks
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Rebecca K. Walters
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Stephanie R. Hare
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Michael B. O’Connor
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- * E-mail: (AJM); (DRG)
| | - David R. Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- * E-mail: (AJM); (DRG)
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24
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Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. J Comput Aided Mol Des 2019; 34:27-37. [PMID: 31773463 DOI: 10.1007/s10822-019-00251-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022]
Abstract
Influenza epidemics are responsible for an average of 3-5 millions of severe cases and up to 500,000 deaths around the world. One of flu pandemic types is influenza A(H1N1)pdm09 virus (pdm09H1N1). Oseltamivir is the antiviral drug used to treat influenza targeting at neuraminidase (NA) located on the viral surface. Influenza virus undergoes high mutation rates and leads to drug resistance, and thus the development of more efficient drugs is required. In the present study, all-atom molecular dynamics simulations were applied to understand the oseltamivir resistance caused by the single E119D and double E119D/H274Y mutations on NA. The obtained results in terms of binding free energy and intermolecular interactions in the ligand-protein interface showed that the oseltamivir could not be well accommodated in the binding pocket of both NA mutants and the 150-loop moves out from oseltamivir as an "open" state. A greater number of water molecules accessible to the binding pocket could disrupt the oseltamivir binding with NA target as seen be high mobility of oseltamivir at the active site. Additionally, our finding could guide to the design and development of novel NA inhibitor drugs.
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25
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Wang K, Lei Z, Zhao L, Chen B, Yang F, Liu K, Zhu H, Zhao H, Cao R, Zhang K, Tian Y. Design, synthesis and biological evaluation of oseltamivir derivatives containing pyridyl group as potent inhibitors of neuraminidase for influenza A. Eur J Med Chem 2019; 185:111841. [PMID: 31708183 DOI: 10.1016/j.ejmech.2019.111841] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022]
Abstract
Influenza A neuraminidase plays an indispensable role in the process of replication and transmission of influenza, so the neuraminidase inhibition can prevent the reproduction of the viruses therefore achieve the effect of treatment of influenza. However, drug resistance of neuraminidase inhibitors such as oseltamivir highlights the need to develop novel structural neuraminidase inhibitors. Here we explored a series of oseltamivir derivatives bearing pyridyl group. Among them, compound 23b exhibiting potent inhibitory activity against neuraminidase from H5N1 subtype was comparable to oseltamivir carboxylate. Cytopathic effect inhibition assay in MDCK cells indicated that compound 23b exerted powerful inhibitions on influenza viruses. And compound 23b were nontoxic to MDCK cells. Meanwhile, compound 23b showed high stability towards rat liver microsomes, human liver microsomes and human plasma. This research enriched the structural type of neuraminidase inhibitors.
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Affiliation(s)
- Kuanglei Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, PR China; School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Zaiqiang Lei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Lei Zhao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China
| | - Binfeng Chen
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Fei Yang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Kemin Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Hongxi Zhu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Hongqian Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, PR China.
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, PR China; School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, 510006, PR China.
| | - Yongshou Tian
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, PR China.
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26
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Jia R, Zhang J, Ai W, Ding X, Desta S, Sun L, Sun Z, Ma X, Li Z, Wang D, Huang B, Zhan P, Liu X. Design, synthesis and biological evaluation of "Multi-Site"-binding influenza virus neuraminidase inhibitors. Eur J Med Chem 2019; 178:64-80. [PMID: 31176096 DOI: 10.1016/j.ejmech.2019.05.076] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/22/2019] [Accepted: 05/27/2019] [Indexed: 11/27/2022]
Abstract
Encouraged by our earlier discovery of neuraminidase inhibitors targeting 150-cavity or 430-cavity, herein, to yield more potent inhibitors, we designed, synthesized, and biologically evaluated a series of novel oseltamivir derivatives via modification of C-1 and C5-NH2 of oseltamivir by exploiting 150-cavity and/or 430-cavity. Among the synthesized compounds, compound 15e, the most potent N1-selective inhibitor targeting 150-cavity, showed 1.5 and 1.8 times greater activity than oseltamivir carboxylate (OSC) against N1 (H5N1) and N1 (H5N1-H274Y). In cellular assays, 15e also exhibited greater potency than OSC against H5N1 with EC50 of 0.66 μM. In addition, 15e demonstrated low cytotoxicity in vitro and low acute toxicity in mice. Molecular docking studies provided insights into the high potency of 15e against N1 and N1-H274Y mutant NA. Overall, we envisioned that the significant breakthrough in the discovery of potent group-1-specific neuraminidase inhibitors may lead to further investigation of more potent anti-influenza agents.
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Affiliation(s)
- Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Wei Ai
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Samuel Desta
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Zhuosen Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 1 Jiaoxiao Road, Jinan, Shandong, 250023, PR China
| | - Zhong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Defeng Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, 1 Jiaoxiao Road, Jinan, Shandong, 250023, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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27
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Ye J, Yang X, Xu M, Chan PKS, Ma C. Novel N-Substituted oseltamivir derivatives as potent influenza neuraminidase inhibitors: Design, synthesis, biological evaluation, ADME prediction and molecular docking studies. Eur J Med Chem 2019; 182:111635. [PMID: 31493744 DOI: 10.1016/j.ejmech.2019.111635] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022]
Abstract
The discovery of novel potent neuraminidase (NA) inhibitors remains an attractive approach for treating infectious diseases caused by influenza. In this study, we describe the design and synthesis of novel N-substituted oseltamivir derivatives for probing the 150-cavity which is nascent to the activity site of NA. NA inhibitory studies showed that new derivatives demonstrated the inhibitory activity with IC50 values at nM level against NA of a clinical influenza virus strain. Moreover, the in silico ADME predictions showed that the selected compounds had comparable properties with oseltamivir carboxylate, which demonstrated the druggablity of these derivatives. Furthermore, molecular docking studies showed that the most potent compound 6f and 10i could adopt different modes of binding interaction with NA, which may provide novel solutions for treating oseltamivir-resistant influenza. Based on the research results, we consider that compounds 6f and 10i have the potential for further studies as novel antiviral agents.
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Affiliation(s)
- Jiqing Ye
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region
| | - Min Xu
- School of Electrical and Data Engineering, Faculty of Engineering and IT, University of Technology Sydney, Sydney, Australia
| | - Paul Kay-Sheung Chan
- Department of Microbiology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong Special Administrative Region; Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.
| | - Cong Ma
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region.
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28
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Zima V, Albiñana CB, Rojíková K, Pokorná J, Pachl P, Řezáčová P, Hudlicky J, Navrátil V, Majer P, Konvalinka J, Kožíšek M, Machara A. Investigation of flexibility of neuraminidase 150-loop using tamiflu derivatives in influenza A viruses H1N1 and H5N1. Bioorg Med Chem 2019; 27:2935-2947. [DOI: 10.1016/j.bmc.2019.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022]
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29
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Bello M. Impact of tetramerization on the ligand recognition of N1 influenza neuraminidase via MMGBSA approach. Biopolymers 2018; 110:e23251. [PMID: 30589081 DOI: 10.1002/bip.23251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 11/09/2022]
Abstract
Influenza virus neuraminidase (NA) is a homotetrameric surface protein that, in contrast to other non-influenza NAs, requires a quaternary assembly to exhibit enzymatic activity, suggesting that the oligomeric state significantly impacts the active site of influenza NA. Nevertheless, most structure-based drug design studies have been reported by employing the monomeric state in the closed or open-loop due to the computational cost of employing the tetrameric NA. In this work, we present MD simulations coupled to the MMGBSA approach of avian N1 type NA in its monomeric and tetrameric closed and open-loop state both with and without the inhibitor oseltamivir and its natural substrate, sialic acid. Structural and energetic analyses revealed that the tetrameric state impacts flexibility as well as the map of interactions participating in stabilizing the protein-ligand complexes with respect to the monomeric state. It was observed that the tetrameric state exerts dissimilar effects in binding affinity, characteristic of positive and negative cooperativity for oseltamivir and sialic acid, respectively. Based on our results, to perform a confident structure-based drug design, as well as to evaluate the impact of key mutations through MD simulations, it is important to consider the tetrameric state closed-loop state.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico
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30
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Shin WJ, Seong BL. Novel antiviral drug discovery strategies to tackle drug-resistant mutants of influenza virus strains. Expert Opin Drug Discov 2018; 14:153-168. [PMID: 30585088 DOI: 10.1080/17460441.2019.1560261] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION The emergence of drug-resistant influenza virus strains highlights the need for new antiviral therapeutics to combat future pandemic outbreaks as well as continuing seasonal cycles of influenza. Areas covered: This review summarizes the mechanisms of current FDA-approved anti-influenza drugs and patterns of resistance to those drugs. It also discusses potential novel targets for broad-spectrum antiviral drugs and recent progress in novel drug design to overcome drug resistance in influenza. Expert opinion: Using the available structural information about drug-binding pockets, research is currently underway to identify molecular interactions that can be exploited to generate new antiviral drugs. Despite continued efforts, antivirals targeting viral surface proteins like HA, NA, and M2, are all susceptible to developing resistance. Structural information on the internal viral polymerase complex (PB1, PB2, and PA) provides a new avenue for influenza drug discovery. Host factors, either at the initial step of viral infection or at the later step of nuclear trafficking of viral RNP complex, are being actively pursued to generate novel drugs with new modes of action, without resulting in drug resistance.
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Affiliation(s)
- Woo-Jin Shin
- a Department of Molecular Microbiology and Immunology, Keck School of Medicine , University of Southern California , Los Angeles , CA , USA
| | - Baik L Seong
- b Department of Biotechnology , College of Life Science and Biotechnology, Yonsei University , Seoul , South Korea.,c Vaccine Translational Research Center , Yonsei University , Seoul , South Korea
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31
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DNA-linked inhibitor antibody assay (DIANA) as a new method for screening influenza neuraminidase inhibitors. Biochem J 2018; 475:3847-3860. [PMID: 30404922 PMCID: PMC6292454 DOI: 10.1042/bcj20180764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 12/25/2022]
Abstract
Influenza neuraminidase is responsible for the escape of new viral particles from the infected cell surface. Several neuraminidase inhibitors are used clinically to treat patients or stockpiled for emergencies. However, the increasing development of viral resistance against approved inhibitors has underscored the need for the development of new antivirals effective against resistant influenza strains. A facile, sensitive, and inexpensive screening method would help achieve this goal. Recently, we described a multiwell plate-based DNA-linked inhibitor antibody assay (DIANA). This highly sensitive method can quantify femtomolar concentrations of enzymes. DIANA also has been applied to high-throughput enzyme inhibitor screening, allowing the evaluation of inhibition constants from a single inhibitor concentration. Here, we report the design, synthesis, and structural characterization of a tamiphosphor derivative linked to a reporter DNA oligonucleotide for the development of a DIANA-type assay to screen potential influenza neuraminidase inhibitors. The neuraminidase is first captured by an immobilized antibody, and the test compound competes for binding to the enzyme with the oligo-linked detection probe, which is then quantified by qPCR. We validated this novel assay by comparing it with the standard fluorometric assay and demonstrated its usefulness for sensitive neuraminidase detection as well as high-throughput screening of potential new neuraminidase inhibitors.
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32
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Zhang J, Poongavanam V, Kang D, Bertagnin C, Lu H, Kong X, Ju H, Lu X, Gao P, Tian Y, Jia H, Desta S, Ding X, Sun L, Fang Z, Huang B, Liang X, Jia R, Ma X, Xu W, Murugan NA, Loregian A, Huang B, Zhan P, Liu X. Optimization of N-Substituted Oseltamivir Derivatives as Potent Inhibitors of Group-1 and -2 Influenza A Neuraminidases, Including a Drug-Resistant Variant. J Med Chem 2018; 61:6379-6397. [PMID: 29965752 DOI: 10.1021/acs.jmedchem.8b00929] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
On the basis of our earlier discovery of N1-selective inhibitors, the 150-cavity of influenza virus neuraminidases (NAs) could be further exploited to yield more potent oseltamivir derivatives. Among the synthesized compounds, 15b and 15c were exceptionally active against both group-1 and -2 NAs. Especially for 09N1, N2, N6, and N9 subtypes, they showed 6.80-12.47 and 1.20-3.94 times greater activity than oseltamivir carboxylate (OSC). They also showed greater inhibitory activity than OSC toward H274Y and E119V variant. In cellular assays, they exhibited greater potency than OSC toward H5N1, H5N2, H5N6, and H5N8 viruses. 15b demonstrated high metabolic stability, low cytotoxicity in vitro, and low acute toxicity in mice. Computational modeling and molecular dynamics studies provided insights into the role of R group of 15b in improving potency toward group-1 and -2 NAs. We believe the successful exploitation of the 150-cavity of NAs represents an important breakthrough in the development of more potent anti-influenza agents.
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Affiliation(s)
- Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M. , Denmark
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Chiara Bertagnin
- Department of Molecular Medicine , University of Padova , via Gabelli 63 , 35121 Padova , Italy
| | - Huamei Lu
- Institute of Poultry Science , Shandong Academy of Agricultural Sciences , 1, Jiaoxiao Road , Jinan , Shandong 250023 , P. R. China
| | - Xiujie Kong
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Han Ju
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Xueyi Lu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Ye Tian
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Haiyong Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Samuel Desta
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Zengjun Fang
- The Second Hospital of Shandong University , no. 247 Beiyuan Avenue , Jinan 250033 , China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Xuewu Liang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Xiuli Ma
- Institute of Poultry Science , Shandong Academy of Agricultural Sciences , 1, Jiaoxiao Road , Jinan , Shandong 250023 , P. R. China
| | - Wenfang Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Natarajan Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology , KTH Royal Institute of Technology , S-106 91 Stockholm , Sweden
| | - Arianna Loregian
- Department of Molecular Medicine , University of Padova , via Gabelli 63 , 35121 Padova , Italy
| | - Bing Huang
- Institute of Poultry Science , Shandong Academy of Agricultural Sciences , 1, Jiaoxiao Road , Jinan , Shandong 250023 , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Jinan , Shandong , P.R. China
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33
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Chen YQ, Wohlbold TJ, Zheng NY, Huang M, Huang Y, Neu KE, Lee J, Wan H, Rojas KT, Kirkpatrick E, Henry C, Palm AKE, Stamper CT, Lan LYL, Topham DJ, Treanor J, Wrammert J, Ahmed R, Eichelberger MC, Georgiou G, Krammer F, Wilson PC. Influenza Infection in Humans Induces Broadly Cross-Reactive and Protective Neuraminidase-Reactive Antibodies. Cell 2018; 173:417-429.e10. [PMID: 29625056 PMCID: PMC5890936 DOI: 10.1016/j.cell.2018.03.030] [Citation(s) in RCA: 298] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/08/2018] [Accepted: 03/09/2018] [Indexed: 12/12/2022]
Abstract
Antibodies to the hemagglutinin (HA) and neuraminidase (NA) glycoproteins are the major mediators of protection against influenza virus infection. Here, we report that current influenza vaccines poorly display key NA epitopes and rarely induce NA-reactive B cells. Conversely, influenza virus infection induces NA-reactive B cells at a frequency that approaches (H1N1) or exceeds (H3N2) that of HA-reactive B cells. NA-reactive antibodies display broad binding activity spanning the entire history of influenza A virus circulation in humans, including the original pandemic strains of both H1N1 and H3N2 subtypes. The antibodies robustly inhibit the enzymatic activity of NA, including oseltamivir-resistant variants, and provide robust prophylactic protection, including against avian H5N1 viruses, in vivo. When used therapeutically, NA-reactive antibodies protected mice from lethal influenza virus challenge even 48 hr post infection. These findings strongly suggest that influenza vaccines should be optimized to improve targeting of NA for durable and broad protection against divergent influenza strains.
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Affiliation(s)
- Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Teddy John Wohlbold
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Yunping Huang
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Karlynn E Neu
- The Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Jiwon Lee
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78731, USA
| | - Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Karla Thatcher Rojas
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Ericka Kirkpatrick
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carole Henry
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Anna-Karin E Palm
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA
| | | | - Linda Yu-Ling Lan
- The Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - David J Topham
- Center for Vaccine Biology & Immunology, Department of Microbiology & Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John Treanor
- Division of Infectious Disease, Department of Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jens Wrammert
- Emory Vaccine Center, Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maryna C Eichelberger
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78731, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, the Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL 60637, USA.
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Mohan S, Pinto BM. Exploration of the 150 cavity and the role of serendipity in the discovery of inhibitors of influenza virus A neuraminidase. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Influenza pandemics are an ongoing threat for the human population, as the avian influenza viruses H5N1 and H7N9 continue to circulate in the bird population and the chance of avian to human transmission increases. Neuraminidase, a glycoprotein located on the surface of the influenza virus, plays a crucial role in the viral replication process and, hence, has proven to be a useful target enzyme for the treatment of influenza infections. The discovery that certain subtypes of influenza neuraminidase have an additional cavity, the 150 cavity, near the substrate binding site has triggered considerable interest in the design of influenza inhibitors that exploit this feature. Currently available antiviral drugs, neuraminidase inhibitors oseltamivir and zanamivir, were designed using crystal structures predating this discovery by some years. This mini review is aimed at summarizing our group’s efforts, together with related work from other groups, on neuraminidase inhibitors that are designed to exploit both the catalytic site and the 150 cavity. The design of a parent scaffold that yields a potent inhibitor that is active in cell culture assays and retains activity against several neuraminidases from mutant strains is also described. Finally, the role of serendipity in the discovery of a new class of potent neuraminidase inhibitors with a novel spirolactam scaffold is also highlighted.
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Affiliation(s)
- Sankar Mohan
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - B. Mario Pinto
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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35
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Screening for Neuraminidase Inhibitor Resistance Markers among Avian Influenza Viruses of the N4, N5, N6, and N8 Neuraminidase Subtypes. J Virol 2017; 92:JVI.01580-17. [PMID: 29046464 DOI: 10.1128/jvi.01580-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 10/09/2017] [Indexed: 12/22/2022] Open
Abstract
Several subtypes of avian influenza viruses (AIVs) are emerging as novel human pathogens, and the frequency of related infections has increased in recent years. Although neuraminidase (NA) inhibitors (NAIs) are the only class of antiviral drugs available for therapeutic intervention for AIV-infected patients, studies on NAI resistance among AIVs have been limited, and markers of resistance are poorly understood. Previously, we identified unique NAI resistance substitutions in AIVs of the N3, N7, and N9 NA subtypes. Here, we report profiles of NA substitutions that confer NAI resistance in AIVs of the N4, N5, N6, and N8 NA subtypes using gene-fragmented random mutagenesis. We generated libraries of mutant influenza viruses using reverse genetics (RG) and selected resistant variants in the presence of the NAIs oseltamivir carboxylate and zanamivir in MDCK cells. In addition, two substitutions, H274Y and R292K (N2 numbering), were introduced into each NA gene for comparison. We identified 37 amino acid substitutions within the NA gene, 16 of which (4 in N4, 4 in N5, 4 in N6, and 4 in N8) conferred resistance to NAIs (oseltamivir carboxylate, zanamivir, or peramivir) as determined using a fluorescence-based NA inhibition assay. Substitutions conferring NAI resistance were mainly categorized as either novel NA subtype specific (G/N147V/I, A246V, and I427L) or previously reported in other subtypes (E119A/D/V, Q136K, E276D, R292K, and R371K). Our results demonstrate that each NA subtype possesses unique NAI resistance markers, and knowledge of these substitutions in AIVs is important in facilitating antiviral susceptibility monitoring of NAI resistance in AIVs.IMPORTANCE The frequency of human infections with avian influenza viruses (AIVs) has increased in recent years. Despite the availability of vaccines, neuraminidase inhibitors (NAIs), as the only available class of drugs for AIVs in humans, have been constantly used for treatment, leading to the inevitable emergence of drug-resistant variants. To screen for substitutions conferring NAI resistance in AIVs of N4, N5, N6, and N8 NA subtypes, random mutations within the target gene were generated, and resistant viruses were selected from mutant libraries in the presence of individual drugs. We identified 16 NA substitutions conferring NAI resistance in the tested AIV subtypes; some are novel and subtype specific, and others have been previously reported in other subtypes. Our findings will contribute to an increased and more comprehensive understanding of the mechanisms of NAI-induced inhibition of influenza virus and help lead to the development of drugs that bind to alternative interaction motifs.
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36
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Exploration of binding and inhibition mechanism of a small molecule inhibitor of influenza virus H1N1 hemagglutinin by molecular dynamics simulation. Sci Rep 2017. [PMID: 28630402 PMCID: PMC5476670 DOI: 10.1038/s41598-017-03719-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Influenza viruses are a major public health threat worldwide. The influenza hemagglutinin (HA) plays an essential role in the virus life cycle. Due to the high conservation of the HA stem region, it has become an especially attractive target for inhibitors for therapeutics. In this study, molecular simulation was applied to study the mechanism of a small molecule inhibitor (MBX2329) of influenza HA. Behaviors of the small molecule under neutral and acidic conditions were investigated, and an interesting dynamic binding mechanism was found. The results suggested that the binding of the inhibitor with HA under neutral conditions facilitates only its intake, while it interacts with HA under acidic conditions using a different mechanism at a new binding site. After a series of experiments, we believe that binding of the inhibitor can prevent the release of HA1 from HA2, further maintaining the rigidity of the HA2 loop and stabilizing the distance between the long helix and short helices. The investigated residues in the new binding site show high conservation, implying that the new binding pocket has the potential to be an effective drug target. The results of this study will provide a theoretical basis for the mechanism of new influenza virus inhibitors.
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37
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Mögling R, Richard MJ, Vliet SVD, Beek RV, Schrauwen EJA, Spronken MI, Rimmelzwaan GF, Fouchier RAM. Neuraminidase-mediated haemagglutination of recent human influenza A(H3N2) viruses is determined by arginine 150 flanking the neuraminidase catalytic site. J Gen Virol 2017; 98:1274-1281. [PMID: 28612701 DOI: 10.1099/jgv.0.000809] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Over the last decade, an increasing proportion of circulating human influenza A(H3N2) viruses exhibited haemagglutination activity that was sensitive to neuraminidase inhibitors. This change in haemagglutination as compared to older circulating A(H3N2) viruses prompted an investigation of the underlying molecular basis. Recent human influenza A(H3N2) viruses were found to agglutinate turkey erythrocytes in a manner that could be blocked with either oseltamivir or neuraminidase-specific antisera, indicating that agglutination was driven by neuraminidase, with a low or negligible contribution of haemagglutinin. Using representative virus recombinants it was shown that the haemagglutinin of a recent A(H3N2) virus indeed had decreased activity to agglutinate turkey erythrocytes, while its neuraminidase displayed increased haemagglutinating activity. Viruses with chimeric and mutant neuraminidases were used to identify the amino acid substitution histidine to arginine at position 150 flanking the neuraminidase catalytic site as the determinant of this neuraminidase-mediated haemagglutination. An analysis of publicly available neuraminidase gene sequences showed that viruses with histidine at position 150 were rapidly replaced by viruses with arginine at this position between 2005 and 2008, in agreement with the phenotypic data. As a consequence of neuraminidase-mediated haemagglutination of recent A(H3N2) viruses and poor haemagglutination via haemagglutinin, haemagglutination inhibition assays with A(H3N2) antisera are no longer useful to characterize the antigenic properties of the haemagglutinin of these viruses for vaccine strain selection purposes. Continuous monitoring of the evolution of these viruses and potential consequences for vaccine strain selection remains important.
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Affiliation(s)
- Ramona Mögling
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Ruud van Beek
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Eefje J A Schrauwen
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands
| | | | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
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38
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Takashita E, Fujisaki S, Shirakura M, Nakamura K, Kishida N, Kuwahara T, Shimazu Y, Shimomura T, Watanabe S, Odagiri T. Influenza A(H1N1)pdm09 virus exhibiting enhanced cross-resistance to oseltamivir and peramivir due to a dual H275Y/G147R substitution, Japan, March 2016. ACTA ACUST UNITED AC 2017; 21:30258. [PMID: 27336226 DOI: 10.2807/1560-7917.es.2016.21.24.30258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022]
Abstract
An influenza A(H1N1)pdm09 virus carrying a G147R substitution in combination with an H275Y substitution in the neuraminidase protein, which confers cross-resistance to oseltamivir and peramivir, was detected from an immunocompromised inpatient in Japan, March 2016. This dual H275Y/G147R mutant virus exhibited enhanced cross-resistance to both drugs compared with the single H275Y mutant virus and reduced susceptibility to zanamivir, although it showed normal inhibition by laninamivir.
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Affiliation(s)
- Emi Takashita
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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39
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Hariono M, Abdullah N, Damodaran K, Kamarulzaman EE, Mohamed N, Hassan SS, Shamsuddin S, Wahab HA. Potential New H1N1 Neuraminidase Inhibitors from Ferulic Acid and Vanillin: Molecular Modelling, Synthesis and in Vitro Assay. Sci Rep 2016; 6:38692. [PMID: 27995961 PMCID: PMC5171792 DOI: 10.1038/srep38692] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/11/2016] [Indexed: 12/30/2022] Open
Abstract
We report the computational and experimental efforts in the design and synthesis of novel neuraminidase (NA) inhibitors from ferulic acid and vanillin. Two proposed ferulic acid analogues, MY7 and MY8 were predicted to inhibit H1N1 NA using molecular docking. From these two analogues, we designed, synthesised and evaluated the biological activities of a series of ferulic acid and vanillin derivatives. The enzymatic H1N1 NA inhibition assay showed MY21 (a vanillin derivative) has the lowest IC50 of 50 μM. In contrast, the virus inhibition assay showed MY15, a ferulic acid derivative has the best activity with the EC50 of ~0.95 μM. Modelling studies further suggest that these predicted activities might be due to the interactions with conserved and essential residues of NA with ΔGbind values comparable to those of oseltamivir and zanamivir, the two commercial NA inhibitors.
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Affiliation(s)
- Maywan Hariono
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Nurshariza Abdullah
- School of Health Sciences, Universiti Sains Malaysia, 16150 Kubang Krian, Kelantan, Malaysia
| | - K.V. Damodaran
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Ezatul E. Kamarulzaman
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Nornisah Mohamed
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Sharifah Syed Hassan
- Jeffry Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Islam, Malaysia
| | - Shaharum Shamsuddin
- School of Health Sciences, Universiti Sains Malaysia, 16150 Kubang Krian, Kelantan, Malaysia
| | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science, Technology and Innovation, Halaman Bukit Gambir, 11900 Bayan Lepas, Pulau Pinang, Malaysia
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40
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Prachanronarong KL, Özen A, Thayer KM, Yilmaz LS, Zeldovich KB, Bolon DN, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Kurt-Yilmaz N, Schiffer CA. Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase. J Chem Theory Comput 2016; 12:6098-6108. [PMID: 27951676 DOI: 10.1021/acs.jctc.6b00703] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neuraminidase (NA) inhibitors are used for the prevention and treatment of influenza A virus infections. Two subtypes of NA, N1 and N2, predominate in viruses that infect humans, but differential patterns of drug resistance have emerged in each subtype despite highly homologous active sites. To understand the molecular basis for the selection of these drug resistance mutations, structural and dynamic analyses on complexes of N1 and N2 NA with substrates and inhibitors were performed. Comparison of dynamic substrate and inhibitor envelopes and interactions at the active site revealed how differential patterns of drug resistance have emerged for specific drug resistance mutations, at residues I222, S246, and H274 in N1 and E119 in N2. Our results show that the differences in intermolecular interactions, especially van der Waals contacts, of the inhibitors versus substrates at the NA active site effectively explain the selection of resistance mutations in the two subtypes. Avoiding such contacts that render inhibitors vulnerable to resistance by better mimicking the dynamics and intermolecular interactions of substrates can lead to the development of novel inhibitors that avoid drug resistance in both subtypes.
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Affiliation(s)
| | | | | | | | | | | | | | - Jeffrey D Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
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41
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Resistance to Mutant Group 2 Influenza Virus Neuraminidases of an Oseltamivir-Zanamivir Hybrid Inhibitor. J Virol 2016; 90:10693-10700. [PMID: 27654293 DOI: 10.1128/jvi.01703-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/11/2016] [Indexed: 12/18/2022] Open
Abstract
Influenza virus neuraminidase (NA) drug resistance is one of the challenges to preparedness against epidemic and pandemic influenza virus infections. NA N1- and N2-containing influenza viruses are the primary cause of seasonal epidemics and past pandemics. The structural and functional basis underlying drug resistance of the influenza virus N1 NA is well characterized. Yet drug resistance of the N2 strain is not well understood. Here, we confirm that replacement of N2 E119 or I222 results in multidrug resistance, and when the replacements occur together, the sensitivity to NA inhibitors (NAI) is reduced severely. Using crystallographic studies, we showed that E119 replacement results in a loss of hydrogen bonding to oseltamivir and zanamivir, whereas I222 replacement results in a change in the hydrophobic environment that is critical for oseltamivir binding. Moreover, we found that MS-257, a zanamivir-oseltamivir hybrid inhibitor, is less susceptible to drug resistance. The binding mode of MS-257 shows that increased hydrogen bonding interactions between the inhibitor and NA active site anchor the inhibitor within the active site and allow adjustments in response to active-site modifications. Such stability is likely responsible for the observed reduced susceptibility to drug resistance. MS-257 serves as a next-generation anti-influenza virus drug candidate and serves also as a scaffold for further design of NAIs. IMPORTANCE Oseltamivir and zanamivir are the two major antiviral drugs available for the treatment of influenza virus infections. However, multidrug-resistant viruses have emerged in clinical cases, which pose a challenge for the development of new drugs. N1 and N2 subtypes exist in the viruses which cause seasonal epidemics and past pandemics. Although N1 drug resistance is well characterized, the molecular mechanisms underlying N2 drug resistance are unknown. A previous report showed that an N2 E119V/I222L dual mutant conferred drug resistance to seasonal influenza virus. Here, we confirm that these substitutions result in multidrug resistance and dramatically reduced sensitivity to NAI. We further elucidate the molecular mechanism underlying N2 drug resistance by solving crystal structures of the N2 E119V and I222L mutants and the dual mutant. Most importantly, we found that a novel oseltamivir-zanamivir hybrid inhibitor, MS-257, remains more effective against drug-resistant N2 and is a promising candidate as a next-generation anti-influenza virus drug.
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42
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Design and synthesis of 1,2,3-triazole-containing N-acyl zanamivir analogs as potent neuraminidase inhibitors. Eur J Med Chem 2016; 123:397-406. [PMID: 27487569 DOI: 10.1016/j.ejmech.2016.07.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/24/2016] [Accepted: 07/25/2016] [Indexed: 12/17/2022]
Abstract
The design of potent metabolically stable neuraminidase (NA) inhibitors represents an attractive approach for treating influenza virus infection. In this study, we describe the exploitation of the 150-cavity in the active site of group 1 NA for the design, synthesis, and in vitro evaluation of new triazole-containing N-acyl derivatives related to Zanamivir. Inhibition studies with influenza virus NAs of group 1 (H1N1) and group 2 (H3N2) revealed that several of them are good inhibitors, with IC50 values in the low nanomolar (2.3 nM-31 nM) range. Substituents that form stable van der Waals interaction with the 150-cavity residues play crucial roles in NA inhibition as demonstrated by the potency of 6a (H1N1 IC50 = 2.3 nM, and H3N2 IC50 = 2.9 nM). Docking studies indicated that the cyclohexane-substituted triazole ring extended toward the hydrophobic region in the active site of group 1 NA in open form. The high potency observed for inhibitor 6a may be attributable to the highly favorable hydrophobic interactions in this region.
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43
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Fu L, Bi Y, Wu Y, Zhang S, Qi J, Li Y, Lu X, Zhang Z, Lv X, Yan J, Gao GF, Li X. Structure-Based Tetravalent Zanamivir with Potent Inhibitory Activity against Drug-Resistant Influenza Viruses. J Med Chem 2016; 59:6303-12. [DOI: 10.1021/acs.jmedchem.6b00537] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lifeng Fu
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, China
- Graduate
University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Yuhai Bi
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Yan Wu
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Shanshan Zhang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Graduate
University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Jianxun Qi
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Yan Li
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Xuancheng Lu
- Laboratory
Animal Center, Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China
| | - Zhenning Zhang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Graduate
University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Xun Lv
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Jinghua Yan
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Center
for Influenza Research and Early Warning, Chinese Academy of Sciences (CASCIRE), Chaoyang District, Beijing 100101, China
| | - George F. Gao
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Center
for Influenza Research and Early Warning, Chinese Academy of Sciences (CASCIRE), Chaoyang District, Beijing 100101, China
| | - Xuebing Li
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, China
- Center
for Influenza Research and Early Warning, Chinese Academy of Sciences (CASCIRE), Chaoyang District, Beijing 100101, China
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44
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Durrant JD, Bush RM, Amaro RE. Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants. J Phys Chem B 2016; 120:8590-9. [PMID: 27141956 PMCID: PMC5002936 DOI: 10.1021/acs.jpcb.6b02655] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Deletions in the
stalk of the influenza neuraminidase (NA) surface
protein are associated with increased virulence, but the mechanisms
responsible for this enhanced virulence are unclear. Here we use microsecond
molecular dynamics simulations to explore the effect of stalk deletion
on enzymatic activity, contrasting NA proteins from the A/swine/Shandong/N1/2009
strain both with and without a stalk deletion. By modeling and simulating
neuraminidase apo glycoproteins embedded in complex-mixture lipid
bilayers, we show that the geometry and dynamics of the neuraminidase
enzymatic pocket may differ depending on stalk length, with possible
repercussions on the binding of the endogenous sialylated-oligosaccharide
receptors. We also use these simulations to predict previously unrecognized
druggable “hotspots” on the neuraminidase surface that
may prove useful for future efforts aimed at structure-based drug
design.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California San Diego , La Jolla, California 92093, United States
| | - Robin M Bush
- Department of Ecology & Evolutionary Biology, University of California Irvine , Irvine, California 92697, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California San Diego , La Jolla, California 92093, United States
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45
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Phylogenetic analysis of human influenza A/H3N2 viruses isolated in 2015 in Germany indicates significant genetic divergence from vaccine strains. Arch Virol 2016; 161:1505-15. [PMID: 26973232 DOI: 10.1007/s00705-016-2815-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
Abstract
Infections by H3N2-type influenza A viruses (IAV) resulted in significant numbers of hospitalization in several countries in 2014-2015, causing disease also in vaccinated individuals and, in some cases, fatal outcomes. In this study, sequence analysis of H3N2 viruses isolated in Germany from 1998 to 2015, including eleven H3N2 isolates collected early in 2015, was performed. Compared to the vaccine strain A/Texas/50/2012 (H3N2), the 2015 strains from Germany showed up to 4.5 % sequence diversity in their HA1 protein, indicating substantial genetic drift. The data further suggest that two distinct phylogroups, 3C.2 and 3C.3, with 1.6-2.3 % and 0.3-2.4 % HA1 nucleotide and amino acid sequence diversity, respectively, co-circulated in Germany in the 2014/2015 season. Distinct glycosylation patterns and amino acid substitutions in the hemagglutinin and neuraminidase proteins were identified, possibly contributing to the unusually high number of H3N2 infections in this season and providing important information for developing vaccines that are effective against both genotypes.
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46
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Yang Z, Wu F, Yuan X, Zhang L, Zhang S. Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies. J Mol Graph Model 2016; 65:27-34. [PMID: 26905206 DOI: 10.1016/j.jmgm.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 01/09/2023]
Abstract
Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs.
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Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China; School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China.
| | - Fei Wu
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, PR China
| | - Lei Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China.
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47
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Liu T, Lu D, Zhang H, Zheng M, Yang H, Xu Y, Luo C, Zhu W, Yu K, Jiang H. Applying high-performance computing in drug discovery and molecular simulation. Natl Sci Rev 2016; 3:49-63. [PMID: 32288960 PMCID: PMC7107815 DOI: 10.1093/nsr/nww003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 12/31/2022] Open
Abstract
In recent decades, high-performance computing (HPC) technologies and supercomputers in China have significantly advanced, resulting in remarkable achievements. Computational drug discovery and design, which is based on HPC and combines pharmaceutical chemistry and computational biology, has become a critical approach in drug research and development and is financially supported by the Chinese government. This approach has yielded a series of new algorithms in drug design, as well as new software and databases. This review mainly focuses on the application of HPC to the fields of drug discovery and molecular simulation at the Chinese Academy of Sciences, including virtual drug screening, molecular dynamics simulation, and protein folding. In addition, the potential future application of HPC in precision medicine is briefly discussed.
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Affiliation(s)
- Tingting Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dong Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hao Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Huaiyu Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiliang Zhu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kunqian Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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48
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Yusuf M, Mohamed N, Mohamad S, Janezic D, Damodaran KV, Wahab HA. H274Y’s Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. J Chem Inf Model 2016; 56:82-100. [DOI: 10.1021/acs.jcim.5b00331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Muhammad Yusuf
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Nornisah Mohamed
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Suriyati Mohamad
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
- School
of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Dusanka Janezic
- Faculty
of Mathematics, Natural Sciences and Information Technologies, University of Primorska, SI-6000 Koper, Slovenia
| | - K. V. Damodaran
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Habibah A. Wahab
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
- Malaysian
Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science, Technology and Innovation, Halaman Bukit Gambir, 11900 Bayan Lepas, Pulau Pinang, Malaysia
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49
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Colombo C, Pinto BM, Bernardi A, Bennet AJ. Synthesis and evaluation of influenza A viral neuraminidase candidate inhibitors based on a bicyclo[3.1.0]hexane scaffold. Org Biomol Chem 2016; 14:6539-53. [DOI: 10.1039/c6ob00999a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the synthesis of constrained oseltamivir analogues designed to mimic the proposed boat conformation of the enzymatic transition state.
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Affiliation(s)
- Cinzia Colombo
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
| | - B. Mario Pinto
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
| | - Anna Bernardi
- Università degli Studi di Milano
- Dipartimento di Chimica
- I-20133 Milano
- Italy
| | - Andrew J. Bennet
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
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50
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Discovery of Influenza A virus neuraminidase inhibitors using support vector machine and Naïve Bayesian models. Mol Divers 2015; 20:439-51. [PMID: 26689205 DOI: 10.1007/s11030-015-9641-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Neuraminidase (NA) is a critical enzyme in the life cycle of influenza virus, which is known as a successful paradigm in the design of anti-influenza agents. However, to date there are no classification models for the virtual screening of NA inhibitors. In this work, we built support vector machine and Naïve Bayesian models of NA inhibitors and non-inhibitors, with different ratios of active-to-inactive compounds in the training set and different molecular descriptors. Four models with sensitivity or Matthews correlation coefficients greater than 0.9 were chosen to predict the NA inhibitory activities of 15,600 compounds in our in-house database. We combined the results of four optimal models and selected 60 representative compounds to assess their NA inhibitory profiles in vitro. Nine NA inhibitors were identified, five of which were oseltamivir derivatives with large C-5 substituents exhibiting potent inhibition against H1N1 NA with IC50 values in the range of 12.9-185.0 nM, and against H3N2 NA with IC50 values between 18.9 and 366.1 nM. The other four active compounds belonged to novel scaffolds, with IC50 values ranging 39.5-63.8 μM against H1N1 NA and 44.5-114.1 μM against H3N2 NA. This is the first time that classification models of NA inhibitors and non-inhibitors are built and their prediction results validated experimentally using in vitro assays.
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