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Bassetti M, Sepulcri C, Giacobbe DR, Fusco L. Treating influenza with neuraminidase inhibitors: an update of the literature. Expert Opin Pharmacother 2024; 25:1163-1174. [PMID: 38935495 DOI: 10.1080/14656566.2024.2370895] [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: 03/29/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
INTRODUCTION Influenza affects individuals of all ages and poses a significant threat during pandemics, epidemics, and sporadic outbreaks. Neuraminidase inhibitors (NAIs) are currently the first choice in the treatment and prevention of influenza, but their use can be hindered by viral resistance. AREAS COVERED This review summarizes current NAIs pharmacological profiles, their current place in therapy, and the mechanisms of viral resistance and outlines possible new indications, ways of administration, and novel candidate NAIs compounds. EXPERT OPINION NAIs represent a versatile group of compounds with diverse administration methods and pharmacokinetics. While the prevalence of influenza virus resistance to NAIs remains low, there is heightened vigilance due to the pandemic potential of influenza. Several novel NAIs and derivatives are currently under assessment at various stages of development for the treatment and prevention of influenza.
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Affiliation(s)
- Matteo Bassetti
- UO Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Chiara Sepulcri
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Daniele Roberto Giacobbe
- UO Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Ludovica Fusco
- UO Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
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2
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Hancková M, Miháliková L, Pastoreková S, Betáková T. Hypoxia alters the immune response in mouse peritoneal macrophages infected with influenza a virus with truncated NS1 protein. Cytokine 2023; 164:156138. [PMID: 36796258 DOI: 10.1016/j.cyto.2023.156138] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/30/2022] [Accepted: 01/19/2023] [Indexed: 02/16/2023]
Abstract
Macrophages are the most abundant cells in infected tissue and are involved in the clearing infection, and immunomodulation of the innate and adaptive immune response. NS80 virus of influenza A virus, which encodes only the first 80 aa of the NS1 protein, suppresses the immune host response and is associated with enhanced pathogenicity. Hypoxia promotes infiltration of peritoneal macrophages into the adipose tissue and production of cytokines. To understand the role of hypoxia in the regulation of immune response, macrophages were infected with A/WSN/33 (WSN) and NS80 virus, and transcriptional profiles of the RIG-I-like receptor signalling pathway and expression of cytokines were evaluated in normoxia and hypoxia. Hypoxia inhibited the proliferation of IC-21 cells, downregulated the RIG-I-like receptor signalling pathway, and inhibited transcriptional activity of IFN-α, IFN-β, IFN-ε, and IFN-λ mRNA in infected macrophages. While transcription of IL-1β and Casp-1 mRNAs were increased in infected macrophages in normoxia, hypoxia resulted in decreased transcription activity of IL-1β and Casp-1 mRNAs. Hypoxia significantly affected expression of the translation factors IRF4, IFN-γ, and CXCL10 involved in regulation of immune response and polarization of the macrophages. The expression of pro-inflammatory cytokines such as sICAM-1, IL-1α, TNF-α, CCL2, CCL3, CXCL12, and M-CSF was to a large extent affected in uninfected and infected macrophages cultivated in hypoxia. The NS80 virus increased the expression of M-CSF, IL-16, CCL2, CCL3, and CXCL12, especially under hypoxia. The results show that hypoxia may play an important role in peritoneal macrophage activation, regulates the innate and adaptive immune response, changes production of pro-inflammatory cytokines, promotes macrophage polarization, and could affect the function of other immune cells.
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Affiliation(s)
- Miriam Hancková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovak Republic
| | - Lucia Miháliková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovak Republic
| | - Silvia Pastoreková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovak Republic
| | - Tatiana Betáková
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovak Republic; Comenius University in Bratislava, Faculty of Natural Sciences, Department of Microbiology and Virology, Bratislava, Slovak Republic.
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Abstract
The neuraminidase (NA) of influenza A and B viruses plays a distinct role in viral replication and has a highly conserved catalytic site. Numerous sialic (neuraminic) acid analogs that competitively bind to the NA active site and potently inhibit enzyme activity have been synthesized and tested. Four NA inhibitors are now licensed in various parts of the world (zanamivir, oseltamivir, peramivir, and laninamivir) to treat influenza A and B infections. NA changes, naturally occurring or acquired under selective pressure, have been shown to reduce drug binding, thereby affecting the effectiveness of NA inhibitors. Drug resistance and other drawbacks have prompted the search for the next-generation NA-targeting therapeutics. One of the promising approaches is the identification of monoclonal antibodies (mAbs) targeting the conserved NA epitopes. Anti-NA mAbs demonstrate Fab-based antiviral activity supplemented with Fc-mediated immune effector functions. Antiviral Fc-conjugates offer another cutting-edge strategy that is based on a multimodal mechanism of action. These novel antiviral agents are composed of a small-molecule NA inhibitor and an Fc-region that simultaneously engages the immune system. The significant advancements made in recent years further support the value of NA as an attractive target for the antiviral development.
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Affiliation(s)
- Larisa Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
| | - Teena Mohan
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
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Campbell AC, Tanner JJ, Krause KL. Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells. Viruses 2021; 13:v13101893. [PMID: 34696326 PMCID: PMC8538103 DOI: 10.3390/v13101893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/02/2022] Open
Abstract
Influenza virus is a highly contagious virus that causes significant human mortality and morbidity annually. The most effective drugs for treating influenza are the neuraminidase inhibitors, but resistance to these inhibitors has emerged, and additional drug discovery research on neuraminidase and other targets is needed. Traditional methods of neuraminidase production from embryonated eggs are cumbersome, while insect cell derived protein is less reflective of neuraminidase produced during human infection. Herein we describe a method for producing neuraminidase from a human cell line, HEK293-6E, and demonstrate the method by producing the neuraminidase from the 1918 H1N1 pandemic influenza strain. This method produced high levels of soluble neuraminidase expression (>3000 EU/mL), was enhanced by including a secretion signal from a viral chemokine binding protein, and does not require co-expression of additional proteins. The neuraminidase produced was of sufficient quantity and purity to support high resolution crystal structure determination. The structure solved using this protein conformed to the previously reported structure. Notably the glycosylation at three asparagine residues was superior in quality to that from insect cell derived neuraminidase. This method of production of neuraminidase should prove useful in further studies, such as the characterisation of inhibitor binding.
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Affiliation(s)
- Ashley C. Campbell
- Department of Biochemistry, University of Otago, 710 Cumberland St., Dunedin 9016, New Zealand;
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, 710 Cumberland St., Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand
- Correspondence:
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Bosshart PD, Kalbermatter D, Bonetti S, Fotiadis D. The making of a potent L-lactate transport inhibitor. Commun Chem 2021; 4:128. [PMID: 36697570 PMCID: PMC9814091 DOI: 10.1038/s42004-021-00564-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/12/2021] [Indexed: 01/28/2023] Open
Abstract
L-lactate is an important metabolite, energy source, and signaling molecule in health and disease. In mammals, its transport across biological membranes is mediated by monocarboxylate transporters (MCTs) of the solute carrier 16 (SLC16) family. Malfunction, overexpression or absence of transporters of this family are associated with diseases such as cancer and type 2 diabetes. Moreover, lactate acts as a signaling molecule and virulence factor in certain bacterial infections. Here, we report the rational, structure-guided identification of potent, nanomolar affinity inhibitors acting on an L-lactate-specific SLC16 homologue from the bacterium Syntrophobacter fumaroxidans (SfMCT). High-resolution crystal structures of SfMCT with bound inhibitors uncovered their interaction mechanism on an atomic level and the role of water molecules in inhibitor binding. The presented systematic approach is a valuable procedure for the identification of L-lactate transport inhibitors. Furthermore, identified inhibitors represent potential tool compounds to interfere with monocarboxylate transport across biological membranes mediated by MCTs.
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Affiliation(s)
- Patrick D. Bosshart
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland ,Present Address: leadXpro AG, Park Innovare, Villigen, Switzerland
| | - David Kalbermatter
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Sara Bonetti
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Dimitrios Fotiadis
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
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6
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Tram G, Poole J, Adams FG, Jennings MP, Eijkelkamp BA, Atack JM. The Acinetobacter baumannii Autotransporter Adhesin Ata Recognizes Host Glycans as High-Affinity Receptors. ACS Infect Dis 2021; 7:2352-2361. [PMID: 34339169 DOI: 10.1021/acsinfecdis.1c00021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acinetobacter baumannii is a significant opportunistic pathogen responsible for infections of the lung, blood, skin, urinary tract, and soft tissues, with some strains exhibiting almost complete resistance to commonly used antibiotics. This multidrug resistance, together with a dearth of new antibiotic development, mean novel methods of treatment and prevention are urgently needed. Although many A. baumannii factors required to colonize the host have been identified, little is known about the specific host molecules recognized by these factors. A. baumannii produces a trimeric autotransporter adhesin known as Ata that has been previously demonstrated to bind components of the host cell's extracellular matrix, which are often heavily glycosylated. We hypothesized that Ata would exhibit lectin activity which would play a role in adherence to the host cell surface. Our biophysical analysis using glycan arrays and surface plasmon resonance demonstrated that Ata binds galactose, N-acetylglucosamine, and galactose (β1-3/4) N-acetylglucosamine with high-affinity. These structures are present on many of the proteins which were previously reported to be bound by Ata. We also demonstrated that the recognition of human plasma fibronectin by Ata requires this ability to bind glycans, as the interaction between Ata and fibronectin does not occur when fibronectin is deglycosylated. This strongly suggests a key role for Ata lectin activity during host adherence. This information will assist in directing the development of new and effective treatments to block host interactions using glycans and/or novel compounds in multidrug resistant A. baumannii infections.
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Affiliation(s)
- Greg Tram
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4215, Australia
| | - Jessica Poole
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4215, Australia
| | - Felise G. Adams
- Molecular Sciences & Technology, College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4215, Australia
| | - Bart A. Eijkelkamp
- Molecular Sciences & Technology, College of Science and Engineering, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - John M. Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4215, Australia
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Nahar N, Turni C, Tram G, Blackall PJ, Atack JM. Actinobacillus pleuropneumoniae: The molecular determinants of virulence and pathogenesis. Adv Microb Physiol 2021; 78:179-216. [PMID: 34147185 DOI: 10.1016/bs.ampbs.2020.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is responsible for high economic losses in swine herds across the globe. Pleuropneumonia is characterized by severe respiratory distress and high mortality. The knowledge about the interaction between bacterium and host within the porcine respiratory tract has improved significantly in recent years. A. pleuropneumoniae expresses multiple virulence factors, which are required for colonization, immune clearance, and tissue damage. Although vaccines are used to protect swine herds against A. pleuropneumoniae infection, they do not offer complete coverage, and often only protect against the serovar, or serovars, used to prepare the vaccine. This review will summarize the role of individual A. pleuropneumoniae virulence factors that are required during key stages of pathogenesis and disease progression, and highlight progress made toward developing effective and broadly protective vaccines against an organism of great importance to global agriculture and food production.
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Affiliation(s)
- Nusrat Nahar
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Greg Tram
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia.
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8
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Ginex T, Luque FJ. Searching for effective antiviral small molecules against influenza A virus: A patent review. Expert Opin Ther Pat 2020; 31:53-66. [PMID: 33012213 DOI: 10.1080/13543776.2020.1831471] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Introduction: Despite the current interest caused by SARS-Cov-2, influenza continues to be one of the most serious health concerns, with an estimated 1 billion cases across the globe, including 3-5 million severe cases and 290,000-650,000 deaths worldwide. Areas covered: This manuscript reviews the efforts made in the development of small molecules for the treatment of influenza virus, primarily focused on patent applications in the last 5 years. Attention is paid to compounds targeting key functional viral proteins, such as the M2 channel, neuraminidase, and hemagglutinin, highlighting the evolution toward new ligands and scaffolds motivated by the emergence of resistant strains. Finally, the discovery of compounds against novel viral targets, such as the RNA-dependent RNA polymerase, is discussed. Expert opinion: The therapeutic potential of antiviral agents is limited by the increasing presence of resistant strains. This should encourage research on novel strategies for therapeutic intervention. In this context, the discovery of arbidol and JNJ7918 against hemagglutinin, and current efforts on RNA-dependent RNA polymerase have disclosed novel opportunities for therapeutic treatment. Studies should attempt to expand the therapeutic arsenal of anti-flu agents, often in combined therapies, to prevent future health challenges caused by influenza virus. Abbreviations: AlphaLISA: amplified luminescent proximity homogeneous assay; HA: hemagglutinin; NA: neuraminidase; RBD: receptor binding domain; RdRp: RNA-dependent RNA polymerase; SA: sialic Acid; TBHQ: tert-butyl hydroquinone; TEVC: two-electrode voltage clamp.
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Affiliation(s)
- Tiziana Ginex
- Translational Medicinal and Biological Chemistry Group, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Biológicas (CIB-CSIC) , Madrid, Spain
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona , Santa Coloma de Gramanet, Spain
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Cuellar-Camacho JL, Bhatia S, Reiter-Scherer V, Lauster D, Liese S, Rabe JP, Herrmann A, Haag R. Quantification of Multivalent Interactions between Sialic Acid and Influenza A Virus Spike Proteins by Single-Molecule Force Spectroscopy. J Am Chem Soc 2020; 142:12181-12192. [PMID: 32538085 DOI: 10.1021/jacs.0c02852] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Multivalency is a key principle in reinforcing reversible molecular interactions through the formation of multiple bonds. The influenza A virus deploys this strategy to bind strongly to cell surface receptors. We performed single-molecule force spectroscopy (SMFS) to investigate the rupture force required to break individual and multiple bonds formed between synthetic sialic acid (SA) receptors and the two principal spike proteins of the influenza A virus (H3N2): hemagglutinin (H3) and neuraminidase (N2). Kinetic parameters such as the rupture length (χβ) and dissociation rate (koff) are extracted using the model by Friddle, De Yoreo, and Noy. We found that a monovalent SA receptor binds to N2 with a significantly higher bond lifetime (270 ms) compared to that for H3 (36 ms). By extending the single-bond rupture analysis to a multibond system of n protein-receptor pairs, we provide an unprecedented quantification of the mechanistic features of multivalency between H3 and N2 with SA receptors and show that the stability of the multivalent connection increases with the number of bonds from tens to hundreds of milliseconds. Association rates (kon) are also provided, and an estimation of the dissociation constants (KD) between the SA receptors to both proteins indicate a 17-fold higher binding affinity for the SA-N2 bond with respect to that of SA-H3. An optimal designed multivalent SA receptor showed a higher binding stability to the H3 protein of the influenza A virus than to the monovalent SA receptor. Our study emphasizes the influence of the scaffold on the presentation of receptors during multivalent binding.
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Affiliation(s)
- Jose Luis Cuellar-Camacho
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Sumati Bhatia
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Valentin Reiter-Scherer
- Department of Physics & IRIS Adlershof, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Daniel Lauster
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany.,Institute for Biology & IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Susanne Liese
- Department of Mathematics, University of Oslo, Moltke Moes vei 35, 1053 Oslo, Norway
| | - Jürgen P Rabe
- Department of Physics & IRIS Adlershof, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Andreas Herrmann
- Institute for Biology & IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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10
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Computational analysis of drug like candidates against Neuraminidase of Human Influenza A virus subtypes. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2019.100284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Chen F, Yang L, Huang Y, Chen Y, Sang H, Duan W, Yang J. Isocorilagin, isolated from Canarium album (Lour.) Raeusch, as a potent neuraminidase inhibitor against influenza A virus. Biochem Biophys Res Commun 2019; 523:183-189. [PMID: 31843192 DOI: 10.1016/j.bbrc.2019.12.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
Canarium album (Lour.) Raeusch (C. album) as a normally medicinal and edible plant has been used widely in Asian countries and is considered a source of phytochemicals that are beneficial to human health. Here, we showed at the first time isocorilagin, a polyphenolic compound isolated from C. album, displayed antiviral activity against diverse strains of influenza A virus (IAV), including A/Puerto Rico/8/34 (H1N1), A/Aichi/2/68 (H3N2) and NA-H274Y (H1N1) with IC50 value of 9.19 ± 1.99, 23.72 ± 2.51 and 4.64 ± 3.01 μM, respectively. Further mechanistic studies revealed that it clearly inhibited neuraminidase activity of IAV and directly influenced the virus release. The molecular docking studies presented isocorilagin could bind to the highly conserved residues in the active sites of NA, implying that isocorilagin may be effective against various influenza strains and not susceptible to produce drug resistance. Taken together, the results strongly suggest that isocorilagin has potential to be an effective, safe and affordable neuraminidase inhibitor against a diverse panel of IAV strains. More importantly, our work expands the biological activities of C. album extracts and provide a new option for the development of anti-influenza drug.
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Affiliation(s)
- Fangzhao Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Luoping Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yingna Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Huiting Sang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Wenjun Duan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Jie Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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12
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Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM. DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs. J Appl Crystallogr 2018; 51:193-199. [PMID: 29507550 PMCID: PMC5822993 DOI: 10.1107/s1600576717015825] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/30/2017] [Indexed: 11/10/2022] Open
Abstract
It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB, 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.
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Affiliation(s)
- Michał L. Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ulica Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Szymon Migacz
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
| | - Witold Rudnicki
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
- Institute of Informatics, University of Białystok, Białystok, Poland
| | - Anna Makal
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ulica Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Jarosław A. Kalinowski
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ralf W. Grosse-Kunstleve
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ulica Żwirki i Wigury 101, Warszawa, 02-089, Poland
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Gajaganti S, Bajpai S, Srivastava V, Singh S. An efficient, room temperature, oxygen radical anion (O2•−) mediated, one-pot, and multicomponent synthesis of spirooxindoles. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The present report highlights an efficient use of oxygen radical anion to promote a room temperature multi-component synthesis of spirooxindoles (4a–4l) under mild reaction conditions. The potassium superoxide (KO2) and tetraethylammonium bromide (TEAB) combination generate the oxygen radical anion in situ to promote this transformation. This method offers a sustainable and direct access to the biologically important spirooxindole derivatives in good to excellent yields.
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Affiliation(s)
- Somaiah Gajaganti
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
| | - Shivam Bajpai
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
| | - Vandana Srivastava
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
| | - Sundaram Singh
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
- Department of Chemistry, Indian Institute of Technology — BHU, Varanasi 221 005, Uttar Pradesh, India
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14
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Allen WJ, Fochtman BC, Balius TE, Rizzo RC. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. J Comput Chem 2017; 38:2641-2663. [PMID: 28940386 DOI: 10.1002/jcc.25052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
Abstract
De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794
| | - Brian C Fochtman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, 94158
| | - Robert C Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794.,Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York, 11794.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, 11794
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15
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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: 38] [Impact Index Per Article: 4.8] [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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16
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Zwitterionic structures: from physicochemical properties toward computer-aided drug designs. Future Med Chem 2016; 8:2245-2262. [DOI: 10.4155/fmc-2016-0176] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Zwitterions, used widely in chemical, biological and medicinal fields, show distinct physicochemical properties relative to ordinary ampholytes, which largely decide their bioavailability and biological activities. In the present manuscript, these properties are discussed in order to facilitate our understanding of zwitterionic structures, followed by various examples of zwitterionic drugs and the critical role these properties play. We specifically focus our discussions on neuraminidase inhibitors (NAIs), which are used in the treatment and prevention of influenza, covering their computer-assisted design, transformation to zwitterionic isomers and interaction mechanisms of NAIs with proteins. The discovery and development of NAIs provide useful insights that may assist in the exploration of new zwitterionic drugs.
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Laborda P, Wang SY, Voglmeir J. Influenza Neuraminidase Inhibitors: Synthetic Approaches, Derivatives and Biological Activity. Molecules 2016; 21:E1513. [PMID: 27845731 PMCID: PMC6274581 DOI: 10.3390/molecules21111513] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022] Open
Abstract
Despite being a common viral disease, influenza has very negative consequences, causing the death of around half a million people each year. A neuraminidase located on the surface of the virus plays an important role in viral reproduction by contributing to the release of viruses from infected host cells. The treatment of influenza is mainly based on the administration of neuraminidase inhibitors. The neuraminidase inhibitors zanamivir, laninamivir, oseltamivir and peramivir have been commercialized and have been demonstrated to be potent influenza viral neuraminidase inhibitors against most influenza strains. In order to create more potent neuraminidase inhibitors and fight against the surge in resistance resulting from naturally-occurring mutations, these anti-influenza drugs have been used as templates for the development of new neuraminidase inhibitors through structure-activity relationship studies. Here, we review the synthetic routes to these commercial drugs, the modifications which have been performed on these structures and the effects of these modifications on their inhibitory activity.
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Affiliation(s)
- Pedro Laborda
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.
| | - Su-Yan Wang
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.
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18
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Liu X, Huang Y, Liang J, Wang J, Shen Y, Li Y, Zhao Y. Characterization of the malaria parasite protein PfTip, a novel invasion-related protein. Mol Med Rep 2016; 13:3303-10. [PMID: 26935027 DOI: 10.3892/mmr.2016.4910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 01/26/2016] [Indexed: 11/06/2022] Open
Abstract
Malaria is one of the most common infective diseases in the world. Invasion of host erythrocytes by the malaria parasite is crucial for pathogen survival and pathogenesis. Various proteins mediate parasite invasion and identification of novel invasion-related proteins may aid in elucidating the underlying molecular mechanism and new intervention strategies for malaria control. This study characterized the PfTip protein, a homolog of the human T‑cell immunomodulatory protein, and examined its function in preventing parasite infection. Bioinformatics analysis and experimental validation were adopted in the present study. Bioinformatics analysis showed that PfTip has a β‑propeller fold in its structure and is highly expressed at the early ring stage. TNFRSF14 was predicted to be a candidate interactant of PfTip. Further analyses showed that PfTip blockage by sera inhibited erythrocyte invasion by the malaria parasite. The protective effect of PfTip was further confirmed through in vivo analysis. To the best of our knowledge, this study is the first to provide evidence on the function of PfTip in erythrocyte parasite invasion. Additional assays involving the receptor of this protein are currently underway.
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Affiliation(s)
- Xuewu Liu
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yuxiao Huang
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jiao Liang
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jun Wang
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yan Shen
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yinghui Li
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Ya Zhao
- Department of Pathogenic Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. J Mol Biol 2015; 428:538-553. [PMID: 26656922 DOI: 10.1016/j.jmb.2015.11.027] [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: 09/28/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 11/22/2022]
Abstract
The therapeutic benefits of the neuraminidase (NA) inhibitor oseltamivir are dampened by the emergence of drug resistance mutations in influenza A virus (IAV). To investigate the mechanistic features that underlie resistance, we developed an approach to quantify the effects of all possible single-nucleotide substitutions introduced into important regions of NA. We determined the experimental fitness effects of 450 nucleotide mutations encoding positions both surrounding the active site and at more distant sites in an N1 strain of IAV in the presence and absence of oseltamivir. NA mutations previously known to confer oseltamivir resistance in N1 strains, including H275Y and N295S, were adaptive in the presence of drug, indicating that our experimental system captured salient features of real-world selection pressures acting on NA. We identified mutations, including several at position 223, that reduce the apparent affinity for oseltamivir in vitro. Position 223 of NA is located adjacent to a hydrophobic portion of oseltamivir that is chemically distinct from the substrate, making it a hotspot for substitutions that preferentially impact drug binding relative to substrate processing. Furthermore, two NA mutations, K221N and Y276F, each reduce susceptibility to oseltamivir by increasing NA activity without altering drug binding. These results indicate that competitive expansion of IAV in the face of drug pressure is mediated by a balance between inhibitor binding and substrate processing.
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20
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Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. DOCK 6: Impact of new features and current docking performance. J Comput Chem 2015; 36:1132-56. [PMID: 25914306 DOI: 10.1002/jcc.23905] [Citation(s) in RCA: 450] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 03/01/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, 11794
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21
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Xie NZ, Du QS, Li JX, Huang RB. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design. PLoS One 2015; 10:e0137113. [PMID: 26339784 PMCID: PMC4560430 DOI: 10.1371/journal.pone.0137113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. METHODS Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. RESULTS The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. CONCLUSION (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.
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Affiliation(s)
- Neng-Zhong Xie
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA, 02478, United States of America
| | - Jian-Xiu Li
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
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22
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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23
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Woods CJ, Shaw KE, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase. J Phys Chem B 2015; 119:997-1001. [PMID: 25340313 DOI: 10.1021/jp506413j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.
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24
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Bodnarchuk MS, Viner R, Michel J, Essex JW. Strategies to calculate water binding free energies in protein-ligand complexes. J Chem Inf Model 2014; 54:1623-33. [PMID: 24684745 DOI: 10.1021/ci400674k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Water molecules are commonplace in protein binding pockets, where they can typically form a complex between the protein and a ligand or become displaced upon ligand binding. As a result, it is often of great interest to establish both the binding free energy and location of such molecules. Several approaches to predicting the location and affinity of water molecules to proteins have been proposed and utilized in the literature, although it is often unclear which method should be used under what circumstances. We report here a comparison between three such methodologies, Just Add Water Molecules (JAWS), Grand Canonical Monte Carlo (GCMC), and double-decoupling, in the hope of understanding the advantages and limitations of each method when applied to enclosed binding sites. As a result, we have adapted the JAWS scoring procedure, allowing the binding free energies of strongly bound water molecules to be calculated to a high degree of accuracy, requiring significantly less computational effort than more rigorous approaches. The combination of JAWS and GCMC offers a route to a rapid scheme capable of both locating and scoring water molecules for rational drug design.
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Affiliation(s)
- Michael S Bodnarchuk
- School of Chemistry, University of Southampton , Highfield, Southampton, SO17 1BJ, U.K
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25
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YANG ZHIWEI, WU FEI, LIU JUNXING, WANG SHUQIU, YUAN XIAOHUI. SUSCEPTIBILITY OF COMMERCIAL NEURAMINIDASE INHIBITORS AGAINST 2013 A/H7N9 INFLUENZA VIRUS: A DOCKING AND MOLECULAR DYNAMICS STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The latest influenza A ( H 7 N 9) virus attracted a worldwide attention due to the first report of human infections and the continuing reported cases in China. In this work, homology modeling, docking and molecular dynamics simulations were combined to study the interactions between neuraminidase ( N 9_2013, from novel A/ H 7 N 9 virus) and agents zanamivir, oseltamivir, peramivir. It was found that N 9_2013 protein is structurally close to the template (PDB code: 1F8B), especially the active site. The binding properties of N 9_2013 protein were nearly identical to those of template. As a result, the three available drugs should be still efficacious for the new emerging A ( H 7 N 9) virus. However, the stabilities of docked complexes and binding affinities (Eint) were slightly reduced, in contrast to the corresponding inhibitor-template complexes, with the values of -82.27 (-84.30), -78.84 (-80.28) and -77.52 (-81.94) kcal mol-1, respectively. Besides, R292K mutation might induce the resistance of the novel virus to the commercial inhibitors. Thus, it arouses the need for continuous monitoring of antiviral drug susceptibilities.
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Affiliation(s)
- ZHIWEI YANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - FEI WU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - JUNXING LIU
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - SHUQIU WANG
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, P. R. China
| | - XIAOHUI YUAN
- Institute of Biomedicine, Jinan University, Guangzhou 510632, P. R. China
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26
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Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. J Comput Aided Mol Des 2013; 27:935-50. [DOI: 10.1007/s10822-013-9691-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/05/2013] [Indexed: 01/15/2023]
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27
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Yuan XH, Wang YC, Qu ZY, Ren JY, Wu XM, Wang JF. Phylogenetic and structural analysis of major surface proteins hemagglutinin and neuraminidase of novel avian influenza virus A H7N9 from chinese patient. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-3200-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Swaminathan K, Dyason JC, Maggioni A, von Itzstein M, Downard KM. Binding of a natural anthocyanin inhibitor to influenza neuraminidase by mass spectrometry. Anal Bioanal Chem 2013; 405:6563-72. [PMID: 23748498 DOI: 10.1007/s00216-013-7068-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/06/2013] [Accepted: 05/15/2013] [Indexed: 10/26/2022]
Abstract
The binding of a natural anthocyanin to influenza neuraminidase has been studied employing mass spectrometry and molecular docking. Derived from a black elderberry extract, cyanidin-3-sambubiocide has been found to be a potent inhibitor of sialidase activity. This study reveals the molecular basis for its activity for the first time. The anthocyanin is shown by parallel experimental and computational approaches to bind in the so-called 430-cavity in the vicinity of neuraminidase residues 356-364 and 395-432. Since this antiviral compound binds remote from Asp 151 and Glu 119, two residues known to regulate neuraminidase resistance, it provides the potential for the development of a new class of antivirals against the influenza virus without this susceptibility.
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Affiliation(s)
- Kavya Swaminathan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
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29
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Park K, Sung NK, Cho AE. Importance of Accurate Charges in Binding Affinity Calculations: A Case of Neuraminidase Series. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.2.545] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Ishimoto T, Jigawa K, Henares TG, Endo T, Hisamoto H. Integration of neuraminidase inhibitor assay into a single-step operation using a combinable poly(dimethylsiloxane) capillary sensor. Analyst 2013; 138:3158-62. [DOI: 10.1039/c3an36785a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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31
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Li L, Li Y, Zhang L, Hou T. Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. J Chem Inf Model 2012; 52:2715-29. [DOI: 10.1021/ci300375k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lin Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Liling Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
- College of
Pharmaceutical Sciences,
Soochow University, Suzhou, Jiangsu 215123, China
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Yamada H, Moriishi E, Haredy AM, Takenaka N, Mori Y, Yamanishi K, Okamoto S. Influenza virus neuraminidase contributes to the dextran sulfate-dependent suppressive replication of some influenza A virus strains. Antiviral Res 2012; 96:344-52. [PMID: 23022352 DOI: 10.1016/j.antiviral.2012.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 08/17/2012] [Accepted: 09/15/2012] [Indexed: 11/29/2022]
Abstract
Dextran sulfate (DS), a negatively charged, sulfated polysaccharide, suppresses the replication of an influenza A virus strain, and this suppression is associated with inhibition of the hemagglutinin (HA)-dependent fusion activity. However, it remains unknown whether the replication of all or just some influenza A virus strains is suppressed by DS, or whether HA is the only target for the replication suppression. In the present study, we found that DS inhibited the replication of some, but not all influenza A virus strains. The suppression in the DS-sensitive strains was dose-dependent and neutralized by diethylaminoethyl-dextran (DD), which has a positive charge. The suppression by DS was observed not only at the initial stage of viral infection, which includes viral attachment and entry, but also at the late stage, which includes virus assembly and release from infected cells. Electron microscopy revealed that the DS induced viral aggregation at the cell surface. The neuraminidase (NA) activity of the strains whose viral replication was inhibited at the late stage was also more suppressed by DS than that of the strains whose replication was not inhibited, and this inhibition of NA activity was also neutralized by adding positively charged DD. Furthermore, we found that replacing the NA gene of a strain in which viral replication was inhibited by DS at the late stage with the NA gene from a strain in which viral replication was not inhibited, eliminated the DS-dependent suppression. These results suggest that the influenza virus NA contributes to the DS-suppressible virus release from infected cells at the late stage, and the suppression may involve the inhibition of NA activity by DS's negative charge.
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Affiliation(s)
- Hiroshi Yamada
- Laboratory of Virology and Vaccinology, Division of Biomedical Research, National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
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Nagae M, Yamaguchi Y. Function and 3D structure of the N-glycans on glycoproteins. Int J Mol Sci 2012; 13:8398-8429. [PMID: 22942711 PMCID: PMC3430242 DOI: 10.3390/ijms13078398] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 06/28/2012] [Accepted: 06/18/2012] [Indexed: 12/17/2022] Open
Abstract
Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the glycan moieties usually have a heterogeneous chemical structure and conformation, and are often mobile. Nonetheless, recent technical advances in glycoprotein crystallography have accelerated the accumulation of 3D structural information. Statistical analysis of “snapshots” of glycoproteins can provide clues to understanding their structural and dynamic aspects. In this review, we provide an overview of crystallographic analyses of glycoproteins, in which electron density of the glycan moiety is clearly observed. These well-defined N-glycan structures are in most cases attributed to carbohydrate-protein and/or carbohydrate-carbohydrate interactions and may function as “molecular glue” to help stabilize inter- and intra-molecular interactions. However, the more mobile N-glycans on cell surface receptors, the electron density of which is usually missing on X-ray crystallography, seem to guide the partner ligand to its binding site and prevent irregular protein aggregation by covering oligomerization sites away from the ligand-binding site.
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Affiliation(s)
| | - Yoshiki Yamaguchi
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-48-467-9619; Fax: +81-48-467-9620
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Du QS, Gao J, Wei YT, Du LQ, Wang SQ, Huang RB. Structure-Based and Multiple Potential Three-Dimensional Quantitative Structure–Activity Relationship (SB-MP-3D-QSAR) for Inhibitor Design. J Chem Inf Model 2012; 52:996-1004. [DOI: 10.1021/ci300066y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qi-Shi Du
- State Key
Laboratory of Non-food Biomass Energy and Enzyme Technology, National
Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007,
China
- Gordon Life Science Institute, San Diego, California, United States
| | - Jing Gao
- Department of Anesthesiology, The Second Hospital of Tianjin Medical University,
Tianjin 300211, China
| | - Yu-Tuo Wei
- State
Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources,
Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
| | - Li-Qin Du
- State
Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources,
Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical
Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ri-Bo Huang
- State Key
Laboratory of Non-food Biomass Energy and Enzyme Technology, National
Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007,
China
- State
Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources,
Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
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Swaminathan K, Downard KM. Anti-Viral Inhibitor Binding to Influenza Neuraminidase by MALDI Mass Spectrometry. Anal Chem 2012; 84:3725-30. [DOI: 10.1021/ac300291c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kavya Swaminathan
- School of Molecular Bioscience University
of Sydney,
Sydney, NSW 2006, Australia
| | - Kevin M. Downard
- School of Molecular Bioscience University
of Sydney,
Sydney, NSW 2006, Australia
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Indu S, Kochat V, Thakurela S, Ramakrishnan C, Varadarajan R. Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets. Proteins 2011; 79:244-60. [PMID: 21058397 DOI: 10.1002/prot.22878] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel β-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T(m). All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG⁰ = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity.
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Affiliation(s)
- S Indu
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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Du QS, Wei H, Huang RB, Chou KC. Progress in structure-based drug design against influenza A virus. Expert Opin Drug Discov 2011; 6:619-31. [PMID: 22646152 DOI: 10.1517/17460441.2011.571671] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The 2009-H1N1 influenza pandemic has prompted new global efforts to develop new drugs and drug design techniques to combat influenza viruses. While there have been a number of attempts to provide drugs to treat influenza, drug resistance has been a major problem with only four drugs currently approved by the FDA for its treatment. AREAS COVERED In this review, the drug-resistant problem of influenza A viruses is discussed and summarized. The article also introduces the experimental and computational structures of drug targeting proteins, neuraminidases, and of the M2 proton channel. Furthermore, the article illustrates the latest drug candidates and techniques of computer-aided drug design with examples of their application, including virtual in silico screening and scoring, AutoDock and evolutionary technique AutoGrow. EXPERT OPINION Structure-based drug design is the inventive process for finding new drugs based on the structural knowledge of the biological target. Computer-aided drug design strategies and techniques will make drug discovery more effective and economical. It is anticipated that the recent advances in structure-based drug design techniques will greatly help scientists to develop more powerful and specific drugs to fight the next generation of influenza viruses.
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Affiliation(s)
- Qi-Shi Du
- Guangxi University, Life Science and Biotechnology College, Nanning, Guangxi, 530004 , China
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Yang Z, Yang G, Zu Y, Fu Y, Zhou L. Computer-based de novo designs of tripeptides as novel neuraminidase inhibitors. Int J Mol Sci 2010; 11:4932-51. [PMID: 21614183 PMCID: PMC3100827 DOI: 10.3390/ijms11124932] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/12/2010] [Accepted: 11/18/2010] [Indexed: 12/22/2022] Open
Abstract
The latest influenza A (H1N1) pandemic attracted worldwide attention and called for the urgent development of novel antiviral drugs. Here, seven tripeptides are designed and explored as neuraminidase (NA) inhibitors on the structural basis of known inhibitors. Their interactions with NA are studied and compared with each other, using flexible docking and molecular dynamics simulations. The various composed tripeptides have respective binding specificities and their interaction energies with NA decrease in the order of FRI > FRV > FRT > FHV > FRS > FRG > YRV (letters corresponding to amino acid code). The Arg and Phe portions of the tripeptides play important roles during the binding process: Arg has strong electrostatic interactions with the key residues Asp151, Glu119, Glu227 and Glu277, whereas Phe fits well in the hydrophobic cave within the NA active site. Owing to the introduction of hydrophobic property, the interaction energies of FRV and FRI are larger; in particular, FRI demonstrates the best binding quality and shows potential as a lead compound. In addition, the influence of the chemical states of the terminal amino acids are clarified: it is revealed that the charged states of the N-terminus (NH(3) (+)) and C-terminus (COO(-)) are crucial for the tripeptide inhibitory activities and longer peptides may not be appropriate. In addition, the medium inhibiting activity by acetylation of the N-terminus indicates the possible chemical modifications of FRI. Experimental efforts are expected in order to actualize the tripeptides as potent NA inhibitors in the near future.
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Affiliation(s)
- Zhiwei Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
| | - Gang Yang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Authors to whom correspondence should be addressed; E-Mails: (G.Y.); (Y.Z.); Tel.: +86-451-82192223; Fax: +86-451-82102082
| | - Yuangang Zu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
- Authors to whom correspondence should be addressed; E-Mails: (G.Y.); (Y.Z.); Tel.: +86-451-82192223; Fax: +86-451-82102082
| | - Yujie Fu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
| | - Lijun Zhou
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; E-Mails: (Z.Y.); (Y.F.); (L.Z.)
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Yang Z, Nie Y, Yang G, Zu Y, Fu Y, Zhou L. Synergistic effects in the designs of neuraminidase ligands: Analysis from docking and molecular dynamics studies. J Theor Biol 2010; 267:363-74. [DOI: 10.1016/j.jtbi.2010.08.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 07/29/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
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Dominiak PM, Volkov A, Dominiak AP, Jarzembska KN, Coppens P. Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme-substrate complex: influenza neuraminidase inhibition. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:485-99. [PMID: 19390154 PMCID: PMC2672818 DOI: 10.1107/s0907444909009433] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 03/13/2009] [Indexed: 11/11/2022]
Abstract
Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor ( approximately -300 kJ mol(-1) for -COO(-) in non-aromatic inhibitors, approximately -120-210 kJ mol(-1) for -COO(-) in aromatic inhibitors and approximately -450 kJ mol(-1) for -PO(3)(2-)) and with the amino and guanidine groups at C4 ( approximately -250 kJ mol(-1)). Other groups contribute less than approximately 100 kJ mol(-1). Residues Glu119, Asp151, Glu227, Glu276 and Arg371 show the largest variation in electrostatic energies of interaction with different groups of inhibitors, which points to their important role in the inhibitor recognition. The Arg292-->Lys mutation reduces the electrostatic interactions of the enzyme with the acidic group at C2 for all inhibitors that have been studied (SIA, DAN, 4AM, ZMR, G20, G28, G39 and BCZ), but enhances the interactions with the glycerol group at C6 for inhibitors that contain it. This is in agreement with the lower level of resistance of the mutated virus to glycerol-containing inhibitors compared with the more hydrophobic derivatives.
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Affiliation(s)
- Paulina M. Dominiak
- Department of Chemistry, State University of New York at Buffalo, NY 14260, USA
- Department of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszawa, Poland
| | - Anatoliy Volkov
- Department of Chemistry, State University of New York at Buffalo, NY 14260, USA
| | - Adam P. Dominiak
- Department of Chemistry, State University of New York at Buffalo, NY 14260, USA
| | | | - Philip Coppens
- Department of Chemistry, State University of New York at Buffalo, NY 14260, USA
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Investigation of atomic level patterns in protein--small ligand interactions. PLoS One 2009; 4:e4473. [PMID: 19221587 PMCID: PMC2637420 DOI: 10.1371/journal.pone.0004473] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 01/07/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Shape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. To date protein-protein, protein-DNA, and protein-RNA interactions were systematically investigated, which is in contrast to interactions with small ligands. We investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes. METHODOLOGY AND PRINCIPAL FINDINGS We show that protein-ligand interactions are governed by different forces for different ligand types, i.e., protein-organic compound interactions are governed by hydrogen bonds, van der Waals contacts, and covalent bonds; protein-metal ion interactions are dominated by electrostatic force and coordination bonds; protein-anion interactions are established with electrostatic force, hydrogen bonds, and van der Waals contacts; and protein-inorganic cluster interactions are driven by coordination bonds. We extracted several frequently occurring atomic-level patterns concerning these interactions. For instance, 73% of investigated covalent bonds were summarized with just three patterns in which bonds are formed between thiol of Cys and carbon or sulfur atoms of ligands, and nitrogen of Lys and carbon of ligands. Similar patterns were found for the coordination bonds. Hydrogen bonds occur in 67% of protein-organic compound complexes and 66% of them are formed between NH- group of protein residues and oxygen atom of ligands. We quantify relative abundance of specific interaction types and discuss their characteristic features. The extracted protein-organic compound patterns are shown to complement and improve a geometric approach for prediction of binding sites. CONCLUSIONS AND SIGNIFICANCE We show that for a given type (group) of ligands and type of the interaction force, majority of protein-ligand interactions are repetitive and could be summarized with several simple atomic-level patterns. We summarize and analyze 10 frequently occurring interaction patterns that cover 56% of all considered complexes and we show a practical application for the patterns that concerns interactions with organic compounds.
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Some novel insights into the binding of oseltamivir and zanamivir to H5N1 and N9 influenza virus neuraminidases: A homology modeling and flexible docking study. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2009. [DOI: 10.2298/jsc0901001m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In the context of the recent pandemic threat by the worldwide spread of H5N1 avian influenza, novel insights into the mechanism of ligand binding and interaction between various inhibitors (zanamivir - ZMV, oseltamivir - OTV, 2,3-didehydro-2-deoxy-N-acetylneuraminic acid - DANA, peramivir - PMV) and neuraminidases (NA) are of vital importance for the structure-based design of new anti-viral drugs. To address this issue, three-dimensional models of H5N1-NA and N9-NA were generated by homology modeling. Traditional residues within the active site throughout the family of NA protein structures were found to be highly conserved in H5N1-NA. A subtle variation between lipophilic and hydrophilic environments in H5N1-NA with respect to N9-NA was observed, thus shedding more light on the high resistance of some H5N1 strains to various NA inhibitors. Based on these models, an ArgusLab4/AScore flexible docking study was performed. The conformational differences between OTV bound to H5N1-NA and OTV bound to N9-NA were structurally identified and quantified. A slight difference of less than 1 kcal mol-1 between the OTV-N9 and OTV-N1 binding free energies is in agreement with the experimentally predicted free energy difference. The conformational differences between ZMV and OTV bound to either H5N1-NA or N9-NA were structurally identified. The binding free energies of the ZMV complexes, being slightly higher than those of OTV, are not in agreement with what was previously proposed using homology modeling. The differences between ZMV and OTV are suggested to be ascribed to the presence/absence of Asn166 in the active cavity of ZMV/OTV in H5N1-NA, and to the presence/absence of Ser165 in the binding site of ZMV/OTV in N9-NA. The charge distribution was evaluated using the semi-empirical AM1 method. The trends of the AM1 charges of the ZMV and OTV side chains in the complexes deviate from those previously reported.
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Yang Z, Yang G, Zu Y, Fu Y, Zhou L. The conformational analysis and proton transfer of neuraminidase inhibitors: a theoretical study. Phys Chem Chem Phys 2009; 11:10035-41. [DOI: 10.1039/b909299d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Viruses, particularly those that are harmful to humans, are the 'silent terrorists' of the twenty-first century. Well over four million humans die per annum as a result of viral infections alone. The scourge of influenza virus has plagued mankind throughout the ages. The fact that new viral strains emerge on a regular basis, particularly out of Asia, establishes a continual socio-economic threat to mankind. The arrival of the highly pathogenic avian influenza H5N1 heightened the threat of a potential human pandemic to the point where many countries have put in place 'preparedness plans' to defend against such an outcome. The discovery of the first designer influenza virus sialidase inhibitor and anti-influenza drug Relenza, and subsequently Tamiflu, has now inspired a number of continuing efforts towards the discovery of next generation anti-influenza drugs. Such drugs may act as 'first-line-of-defence' against the spread of influenza infection and buy time for necessary vaccine development particularly in a human pandemic setting. Furthermore, the fact that influenza virus can develop resistance to therapeutics makes these continuing efforts extremely important. An overview of the role of the virus-associated glycoprotein sialidase (neuraminidase) and some of the most recent developments towards the discovery of anti-influenza drugs based on the inhibition of influenza virus sialidase is provided in this chapter.
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Obiol-Pardo C, Rubio-Martinez J. Homology modeling of human transketolase: description of critical sites useful for drug design and study of the cofactor binding mode. J Mol Graph Model 2008; 27:723-34. [PMID: 19111488 DOI: 10.1016/j.jmgm.2008.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 11/07/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
Abstract
Transketolase, the most critical enzyme of the non-oxidative branch of the pentose phosphate pathway, has been reported as a new target protein for cancer research. However, since the crystal structure of human Transketolase is unknown, no structure-based methods can be used to identify new inhibitors. We performed homology modeling of human Transketolase using the crystal structure of yeast as a template, and then refined the model through molecular dynamics simulations. Based on the resulting structure we propose five critical sites containing arginines (Arg 101, Arg 318, Arg 395, Arg 401 and Arg 474) that contribute to dimer stability or catalytic activity. In addition, an interaction analysis of its cofactor (thiamine pyrophosphate) and a binding site description were carried out, suggesting the substrate channel already identified in yeast Transketolase. A binding free energy calculation of its cofactor was performed to establish the main driving forces of binding. In summary, we describe a reliable model of human Transketolase that can be used in structure-based drug design and in the search for new Transketolase inhibitors that disrupt dimer stability and cover the critical sites found.
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Affiliation(s)
- Cristian Obiol-Pardo
- Dept. de Química Física, Universitat de Barcelona and The Institut de Recerca en Química Teòrica i Computacional (IQTCUB), Martí i Franqués 1, E-08028 Barcelona, Spain
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Chachra R, Rizzo RC. Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. J Chem Theory Comput 2008; 4:1526-40. [DOI: 10.1021/ct800068v] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ricky Chachra
- Department of Applied Mathematics and Statistics, and the Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York 11794
| | - Robert C. Rizzo
- Department of Applied Mathematics and Statistics, and the Institute for Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York 11794
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Hill AD, Reilly PJ. A Gibbs free energy correlation for automated docking of carbohydrates. J Comput Chem 2008; 29:1131-41. [PMID: 18074341 DOI: 10.1002/jcc.20873] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large binding data set has been assembled from the literature. The data set contains information from 262 unique protein-carbohydrate crystal structures for which experimental binding information is known. Hydrogen atoms were added to the structures and training conformations were generated with the automated docking program AutoDock 3.06, resulting in a training set of 225,920 all-atom conformations. In all, 288 formulations of the AutoDock 3.0 free energy model were trained against the data set, testing each of four alternate methods of computing the van der Waals, solvation, and hydrogen-bonding energetic components. The van der Waals parameters from AutoDock 1 produced the lowest errors, and an entropic model derived from statistical mechanics produced the only models with five physically and statistically significant coefficients. Eight models predict the Gibbs free energy of binding with an error of less than 40% of the error of any similar models previously published.
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Affiliation(s)
- Anthony D Hill
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
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Muthas D, Sabnis YA, Lundborg M, Karlén A. Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering. J Mol Graph Model 2007; 26:1237-51. [PMID: 18203638 DOI: 10.1016/j.jmgm.2007.11.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 11/16/2007] [Accepted: 11/21/2007] [Indexed: 10/22/2022]
Abstract
We have investigated the influence of post-filtering virtual screening results, with pharmacophoric features generated from an X-ray structure, on enrichment rates. This was performed using three docking softwares, zdock+, Surflex and FRED, as virtual screening tools and pharmacophores generated in UNITY from co-crystallized complexes. Sets of known actives along with 9997 pharmaceutically relevant decoy compounds were docked against six chemically diverse protein targets namely CDK2, COX2, ERalpha, fXa, MMP3, and NA. To try to overcome the inherent limitations of the well-known docking problem, we generated multiple poses for each compound. The compounds were first ranked according to their scores alone and enrichment rates were calculated using only the top scoring pose of each compound. Subsequently, all poses for each compound were passed through the different pharmacophores generated from co-crystallized complexes and the enrichment factors were re-calculated based on the top-scoring passing pose of each compound. Post-filtering with a pharmacophore generated from only one X-ray complex was shown to increase enrichment rates in all investigated targets compared to docking alone. This indicates that this is a general method, which works for diverse targets and different docking softwares.
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Affiliation(s)
- Daniel Muthas
- Department of Medicinal Chemistry, Division of Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
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Du QS, Wang SQ, Chou KC. Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Biochem Biophys Res Commun 2007; 362:525-31. [PMID: 17707775 DOI: 10.1016/j.bbrc.2007.08.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 08/03/2007] [Indexed: 10/23/2022]
Abstract
The worldwide spread of H5N1 avian influenza and the increasing reports about its resistance to the existing drugs have made a priority for the development of the new anti-influenza molecules. The crystal structure of H5N1 avian influenza neuraminidase reported recently by Russell et al. [R.J. Russell, L.F. Haire, D.J. Stevens, P.J. Collins, Y. P. Lin, G.M. Blackburn, A.J. Hay, S.J. Gamblin, J.J. Skehel, The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design, Nature 443 (2006) 45-49] have provided new opportunities for drug design in this regard. It is revealed through the structure that the active sites of the group-1 neuraminidases, which contain the N1 subtype, have a very different three-dimensional structure from those of group-2 neuraminidases. The key difference is in the 150-loop cavity adjacent to the conserved active site in neuraminidase. Based on these findings and by modifying oseltamivir, six analog inhibitors were proposed as candidates for developing inhibitors against H5N1 virus, particularly against the oseltamivir-resistant H5N1 virus strain.
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Affiliation(s)
- Qi-Shi Du
- Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi 530004, China
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