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Wang K, Zhang H, Tian Y. The current strategies of optimization of oseltamivir against mutant neuraminidases of influenza A:A review. Eur J Med Chem 2022; 243:114711. [DOI: 10.1016/j.ejmech.2022.114711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/14/2022] [Accepted: 08/22/2022] [Indexed: 11/04/2022]
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2
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Schmitz U, Swaminathan S. Discovery and development of oseltamivir at Gilead Sciences. Antivir Ther 2022; 27:13596535211067598. [PMID: 35499178 DOI: 10.1177/13596535211067598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
John Martin's untimely death in March 2021 was a huge loss for us personally, Gilead Sciences, the company he built over 30 years and the scientific community concerned with antiviral therapies. We wish to honor John's legacy by retelling the discovery and history of Tamiflu and his contributions to it. Without his vision, persistence, and keen eye for opportunities, Tamiflu would not exist and Gilead's path would not have been the same. His strategic thinking around the first oral flu drug is still quite relevant today, when we are still in the SARS-CoV-2 pandemic. John explained it simply in an interview with the Science History Institute in May 2020: "…most of my colleagues, we travel with Tamiflu when we go internationally, because it works for treatment and prevention, and hopefully, there will be a solution like that, eventually, for the Covid virus in addition to vaccines. Most people will get a flu vaccine every year, but there is still disease, we need a pill for treatment and prevention.".
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Affiliation(s)
- Uli Schmitz
- 2158Gilead Sciences Inc, Foster City, CA, USA
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Li Y, Kong Y, Zhang M, Yan A, Liu Z. Using Support Vector Machine (SVM) for Classification of Selectivity of H1N1 Neuraminidase Inhibitors. Mol Inform 2016; 35:116-24. [DOI: 10.1002/minf.201500107] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/30/2015] [Indexed: 11/12/2022]
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Discovery of Influenza A virus neuraminidase inhibitors using support vector machine and Naïve Bayesian models. Mol Divers 2015; 20:439-51. [PMID: 26689205 DOI: 10.1007/s11030-015-9641-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Neuraminidase (NA) is a critical enzyme in the life cycle of influenza virus, which is known as a successful paradigm in the design of anti-influenza agents. However, to date there are no classification models for the virtual screening of NA inhibitors. In this work, we built support vector machine and Naïve Bayesian models of NA inhibitors and non-inhibitors, with different ratios of active-to-inactive compounds in the training set and different molecular descriptors. Four models with sensitivity or Matthews correlation coefficients greater than 0.9 were chosen to predict the NA inhibitory activities of 15,600 compounds in our in-house database. We combined the results of four optimal models and selected 60 representative compounds to assess their NA inhibitory profiles in vitro. Nine NA inhibitors were identified, five of which were oseltamivir derivatives with large C-5 substituents exhibiting potent inhibition against H1N1 NA with IC50 values in the range of 12.9-185.0 nM, and against H3N2 NA with IC50 values between 18.9 and 366.1 nM. The other four active compounds belonged to novel scaffolds, with IC50 values ranging 39.5-63.8 μM against H1N1 NA and 44.5-114.1 μM against H3N2 NA. This is the first time that classification models of NA inhibitors and non-inhibitors are built and their prediction results validated experimentally using in vitro assays.
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Synthesis of densely functionalized cispentacin derivatives through selective aziridination and aziridine opening reactions: orthogonally protected di- and triaminocyclopentanecarboxylates. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Cheng LP, Huang XY, Wang Z, Kai ZP, Wu FH. Combined 3D-QSAR, molecular docking, and molecular dynamics study on potent cyclohexene-based influenza neuraminidase inhibitors. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-014-1176-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kiss L, Fülöp F. Synthesis of carbocyclic and heterocyclic β-aminocarboxylic acids. Chem Rev 2013; 114:1116-69. [PMID: 24299148 DOI: 10.1021/cr300454h] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Loránd Kiss
- Institute of Pharmaceutical Chemistry, University of Szeged , H-6720 Szeged, Eötvös utca 6, Hungary
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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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9
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Selective nitrile oxide dipolar cycloaddition for the synthesis of highly functionalized β-aminocyclohexanecarboxylate stereoisomers. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.09.085] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sharma N, Yap CW. Consensus QSAR model for identifying novel H5N1 inhibitors. Mol Divers 2012; 16:513-24. [DOI: 10.1007/s11030-012-9384-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 06/25/2012] [Indexed: 11/24/2022]
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Kiss L, Forró E, Fülöp F. Selective syntheses of novel highly functionalized β-aminocyclohexanecarboxylic acids. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.12.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Reddy BS, Reddy AB, Reddy GR, Reddy PR. Synthesis and Antibacterial Activity of Novel [3-(4-substitutedphenylamino)-8-azabicyclo [3.2.1] oct-8yl]-phenyl-methanone Derivatives. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2011. [DOI: 10.5012/jkcs.2011.55.6.969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Craig IR, Pfleger C, Gohlke H, Essex JW, Spiegel K. Pocket-space maps to identify novel binding-site conformations in proteins. J Chem Inf Model 2011; 51:2666-79. [PMID: 21910474 DOI: 10.1021/ci200168b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer(PCA) approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer(PCA) for rationalizing and improving the understanding of the molecular basis of protein-ligand interaction and bioactivity. A Python program implementing the PocketAnalyzer(PCA) approach is available for download under an open-source license ( http://sourceforge.net/projects/papca/ or http://cpclab.uni-duesseldorf.de/downloads ).
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Affiliation(s)
- Ian R Craig
- Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, UK.
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Magano J. Synthetic Approaches to the Neuraminidase Inhibitors Zanamivir (Relenza) and Oseltamivir Phosphate (Tamiflu) for the Treatment of Influenza. Chem Rev 2009; 109:4398-438. [DOI: 10.1021/cr800449m] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Javier Magano
- Pfizer Global Research & Development, Eastern Point Road, Groton, Connecticut 06340
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Abu Hammad AM, Taha MO. Pharmacophore Modeling, Quantitative Structure−Activity Relationship Analysis, and Shape-Complemented in Silico Screening Allow Access to Novel Influenza Neuraminidase Inhibitors. J Chem Inf Model 2009; 49:978-96. [DOI: 10.1021/ci8003682] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Areej M. Abu Hammad
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Mutasem O. Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
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Abu Hammad AM, Afifi FU, Taha MO. Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions. J Mol Graph Model 2007; 26:443-56. [PMID: 17360207 DOI: 10.1016/j.jmgm.2007.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 02/05/2007] [Accepted: 02/06/2007] [Indexed: 11/15/2022]
Abstract
In this project, several docking conditions, scoring functions and corresponding protein-aligned molecular field analysis (CoMFA) models were evaluated for a diverse set of neuraminidase (NA) inhibitors. To this end, a group of inhibitors were docked into the active site of NA. The docked structures were utilized to construct a corresponding protein-aligned CoMFA models by employing probe-based (H+, OH, CH3) energy grids and genetic partial least squares (G/PLS) statistical analysis. A total of 16 different docking configurations were evaluated, of which some succeeded in producing self-consistent and predictive CoMFA models. However, the best model coincided with docking the ionized ligands into the hydrated form of the binding site via PLP1 scoring function (r2LOO=0.735, r2PRESS against 24 test compounds=0.828). The highest-ranking CoMFA models were employed to probe NA-ligand interactions. Further validation by comparison with a co-crystallized ligand-NA crystallographic structure was performed. This combination of docking/scoring/CoMFA modeling provided interesting insights into the binding of different NA inhibitors.
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Affiliation(s)
- Areej M Abu Hammad
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Queen Rania Street, Amman 11942, Jordan
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Influenza Neuraminidase Inhibitors as Antiviral Agents. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2006. [DOI: 10.1016/s0065-7743(06)41019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Advances in Chemical Synthesis of Carbasugars and Analogues. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1572-5995(03)80013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Hanessian S, Wang J, Montgomery D, Stoll V, Stewart KD, Kati W, Maring C, Kempf D, Hutchins C, Laver WG. Design, synthesis, and neuraminidase inhibitory activity of GS-4071 analogues that utilize a novel hydrophobic paradigm. Bioorg Med Chem Lett 2002; 12:3425-9. [PMID: 12419376 DOI: 10.1016/s0960-894x(02)00732-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Structure-based design has led to the synthesis of a novel analogue of GS-4071, an influenza neuraminidase inhibitor, in which the basic amino group has been replaced by a hydrophobic vinyl group. An X-ray co-crystal structure of the new inhibitor (K(i)=45 nM) bound to the active site shows that the vinyl group occupies the same subsite as the amino group in GS-4071.
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Carrel F, Vogel P. Total synthesis of a protected form of 2,6-anhydro-5-azido-3,5-dideoxy-2-C-hydroxymethyl-l-allo-heptose; a potential precursor of analogs of C-glycosides of neuraminic acid. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0957-4166(00)00460-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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