In silico virtual screening approaches for anti-viral drug discovery

Neumann, 2009, Emergence and pandemic potential of swine-origin H1N1 influenza virus, Nature, 459, 931, 10.1038/nature08157

McInnes, 2007, Virtual screening strategies in drug discovery, Curr. Opin. Chem. Biol., 11, 494, 10.1016/j.cbpa.2007.08.033

Kirchmair, 2011, Development of anti-viral agents using molecular modeling and virtual screening techniques, Infect. Disorders Drug Targets, 11, 64, 10.2174/187152611794407782

Berman, 2002, The Protein Data Bank, Acta Crystallogr. D, 58, 899, 10.1107/S0907444902003451

Kalyaanamoorthy, 2011, Structure-based drug design to augment hit discovery, Drug Discov. Today, 16, 831, 10.1016/j.drudis.2011.07.006

Rarey, 1996, A fast flexible docking method using an incremental construction algorithm, J. Mol. Biol., 261, 470, 10.1006/jmbi.1996.0477

Ewing, 2001, DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases, J. Comput. Aided Mol. Des., 15, 411, 10.1023/A:1011115820450

McGann, 2003, Gaussian docking functions, Biopolymers, 68, 76, 10.1002/bip.10207

Jones, 1997, Development and validation of a genetic algorithm for flexible docking, J. Mol. Biol., 267, 727, 10.1006/jmbi.1996.0897

Morris, 1998, Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, J. Comput. Chem., 19, 1639, 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B

Halgren, 2004, Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening, J. Med. Chem., 47, 1750, 10.1021/jm030644s

Venkatachalam, 2003, LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites, J. Mol. Graphics Model., 21, 289, 10.1016/S1093-3263(02)00164-X

Jain, 2003, Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine, J. Med. Chem., 46, 499, 10.1021/jm020406h

Warren, 2006, A critical assessment of docking programs and scoring functions, J. Med. Chem., 49, 5912, 10.1021/jm050362n

Noha, 2012, Pharmacophore-based discovery of a novel cytosolic phospholipase A(2)alpha inhibitor, Bioorg. Med. Chem. Lett., 22, 1202, 10.1016/j.bmcl.2011.11.093

Distinto, 2012, Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach, Eur. J. Med. Chem., 50, 216, 10.1016/j.ejmech.2012.01.056

Waltenberger, 2011, Pharmacophore modeling and virtual screening for novel acidic inhibitors of microsomal prostaglandin E-2 synthase-1 (mPGES-1), J. Med. Chem., 54, 3163, 10.1021/jm101309g

Schuster, 2011, Pharmacophore-based discovery of FXR agonists. Part I. Model development and experimental validation, Bioorg. Med. Chem., 19, 7168, 10.1016/j.bmc.2011.09.056

Schuster, 2011, Identification of chemically diverse, novel inhibitors of 17 beta-hydroxysteroid dehydrogenase type 3 and 5 by pharmacophore-based virtual screening, J. Steroid Biochem. Mol. Biol., 125, 148, 10.1016/j.jsbmb.2011.01.016

Noha, 2011, Discovery of a novel IKK-beta inhibitor by ligand-based virtual screening techniques, Bioorg. Med. Chem. Lett., 21, 577, 10.1016/j.bmcl.2010.10.051

Seidel, 2010, Strategies for 3D pharmacophore-based virtual screening, Drug Discov. Today: Technol., 7, e221, 10.1016/j.ddtec.2010.11.004

Wolber, 2006, Efficient overlay of small organic molecules using 3D pharmacophores, J. Comput. Aided Mol. Des., 20, 773, 10.1007/s10822-006-9078-7

Wolber, 2005, LigandScout: 3-d pharmacophores derived from protein-bound: ligands and their use as virtual screening filters, J. Chem. Inform. Model., 45, 160, 10.1021/ci049885e

Guner, 2004, Pharmacophore modeling and three dimensional database searching for drug design using catalyst: recent advances, Curr. Med. Chem., 11, 2991, 10.2174/0929867043364036

Cheong, 2011, Pharmacophore elucidation for a new series of 2-aryl-pyrazolo-triazolo-pyrimidines as potent human A(3) adenosine receptor antagonists, Bioorg. Med. Chem. Lett., 21, 2898, 10.1016/j.bmcl.2011.03.073

Dixon, 2006, PHASE: A novel approach to pharmacophore modeling and 3D database searching, Chem. Biol. Drug Design, 67, 370, 10.1111/j.1747-0285.2006.00384.x

Grant, 1996, A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape, J. Comput. Chem., 17, 1653, 10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K

Monto, 2009, The risk of seasonal and pandemic influenza: prospects for control, Clin. Infect. Dis., 48, S20, 10.1086/591853

Gong, 2007, Structure and functions of influenza virus neuraminidase, Curr. Med. Chem., 14, 113, 10.2174/092986707779313444

Kirchmair, 2011, Novel neuraminidase inhibitors: identification, biological evaluation and investigations of the binding mode, Future Med. Chem., 3, 437, 10.4155/fmc.10.292

Bustanji, 2009, In silico screening for non-nucleoside HIV-1 reverse transcriptase inhibitors using physicochemical filters and high-throughput docking followed by in vitro evaluation, Chem. Biol. Drug Design, 74, 258, 10.1111/j.1747-0285.2009.00852.x

Irwin, 2005, ZINC – a free database of commercially available compounds for virtual screening, J. Chem. Inform. Model., 45, 177, 10.1021/ci049714+

Nichols, 2009, Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures, J. Chem. Inform. Model., 49, 1272, 10.1021/ci900068k

Distinto, 2012, Synthesis and biological assessment of novel 2-thiazolylhydrazones and computational analysis of their recognition by monoamine oxidase B, Eur. J. Med. Chem., 48, 284, 10.1016/j.ejmech.2011.12.027

Rajamaki, 2009, Exploration of novel thiobarbituric acid-, rhodanine- and thiohydantoin-based HIV-1 integrase inhibitors, Bioorg. Med. Chem. Lett., 19, 3615, 10.1016/j.bmcl.2009.04.132

LaLonde, 2011, Design, synthesis and biological evaluation of small molecule inhibitors of CD4-gp120 binding based on virtual screening, Bioorg. Med. Chem., 19, 91, 10.1016/j.bmc.2010.11.049

Curreli, 2011, Virtual screening based identification of novel small-molecule inhibitors targeted to the HIV-1 capsid, Bioorg. Med. Chem., 19, 77, 10.1016/j.bmc.2010.11.045

Yennamalli, 2009, Identification of novel target sites and an inhibitor of the dengue virus E protein, J. Comput. Aided Mol. Des., 23, 333, 10.1007/s10822-009-9263-6

Fusco, 2012, Novel therapies for hepatitis C: insights from the structure of the virus, Annu. Rev. Med., 63, 373, 10.1146/annurev-med-042010-085715

Kampmann, 2009, In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses, Antiviral Res., 84, 234, 10.1016/j.antiviral.2009.09.007

Wang, 2009, A small-molecule dengue virus entry inhibitor, Antimicrob. Agents Chemother., 53, 1823, 10.1128/AAC.01148-08

Poh, 2009, A small molecule fusion inhibitor of dengue virus, Antiviral Res., 84, 260, 10.1016/j.antiviral.2009.09.011

Umamaheswari, 2011, Docking studies towards exploring antiviral compounds against envelope protein of yellow fever virus, Interdiscip. Sci. Comput. Life Sci., 3, 64, 10.1007/s12539-011-0064-y

Takaya, 2011, A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors, Bioorg. Med. Chem., 19, 6892, 10.1016/j.bmc.2011.09.023

Shiryaev, 2011, Virtual ligand screening of the National Cancer Institute (NCI) compound library leads to the allosteric inhibitory scaffolds of the west Nile virus NS3 proteinase, Assay Drug Dev. Technol., 9, 69, 10.1089/adt.2010.0309

Kim, 2011, Discovery of novel HCV polymerase inhibitors using pharmacophore-based virtual screening, Bioorg. Med. Chem. Lett., 21, 3329, 10.1016/j.bmcl.2011.04.010

Lin, 2011, Efficient in silico assay of inhibitors of hepatitis C virus RNA-dependent RNA polymerase by structure-based virtual screening and in vitro evaluation, Assay Drug Dev. Technol., 9, 290, 10.1089/adt.2010.0341

Talele, 2010, Structure-based virtual screening, synthesis and SAR of novel inhibitors of hepatitis C virus NS5B polymerase, Bioorg. Med. Chem., 18, 4630, 10.1016/j.bmc.2010.05.030

Musmuca, 2010, Combining 3-D quantitative structure-activity relationship with ligand based and structure based alignment procedures for in silico screening of new hepatitis C virus NS5B polymerase inhibitors, J. Chem. Inform. Model., 50, 662, 10.1021/ci9004749

Podvinec, 2010, Novel inhibitors of dengue virus methyltransferase: discovery by in vitro-driven virtual screening on a desktop computer grid, J. Med. Chem., 53, 1483, 10.1021/jm900776m

Li, 2010, Discovery of selective inhibitors against EBNA1 via high throughput in silico virtual screening, PLoS One, 5

Nguyen, 2011, Virtual screening identification of novel severe acute respiratory syndrome 3C-like protease inhibitors and in vitro confirmation, Bioorg. Med. Chem. Lett., 21, 3088, 10.1016/j.bmcl.2011.03.034

Mukherjee, 2011, Inhibitors of SARS-3CL(pro): virtual screening, biological evaluation, and molecular dynamics simulation studies, J. Chem. Inform. Model., 51, 1376, 10.1021/ci1004916

Park, 2011, Identification of RNA pseudoknot-binding ligand that inhibits the −1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening (vol. 133, p. 10094, 2011), J. Am. Chem. Soc., 133, 14150, 10.1021/ja206172p

Perez-Nueno, 2009, Discovery of novel HIV entry inhibitors for the CXCR4 receptor by prospective virtual screening, J. Chem. Inform. Model., 49, 810, 10.1021/ci800468q