Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking

Ekonomiuk, Dariusz; Su, Xun‐Cheng; Ozawa, Kiyoshi; Bodenreider, Christophe; Lim, Siew Pheng; Yin, Zheng; Keller, Thomas H.; Beer, David; Patel, Viral; Otting, Gottfried; Caflisch, Amedeo; Huang, Danzhi

doi:10.1371/journal.pntd.0000356

Cited by 72 publications

(74 citation statements)

References 62 publications

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“…In fact, we have observed an error of about 1 kcal/mol for 13 and 29 peptidic inhibitors of b-secretase and HIV-1 protease, respectively. 45 Similar accuracy has been reported for other proteases 63,64 and five kinases. 65 …”

Section: Liece Binding Energy Evaluationsupporting

confidence: 81%

“…[94][95][96][97] We have run two in silico screening campaigns to identify inhibitors of the West Nile virus NS3 protease. The first high-throughput docking campaign (Figure 3, left) was performed on the X-ray structure of the protease 64 while the second campaign ( Figure 3, right) made use of a snapshot selected along a 1 ns explicit solvent molecular dynamics simulation started from the crystal structure. 98 This snapshot was chosen from a set of 100 as it optimally accommodates three representative molecular fragments: benzene and two functional groups with a positive charge.…”

Section: West Nile Virus Ns3 Protease (Flaviviral Infections)mentioning

confidence: 99%

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Library screening by fragment‐based docking

Huang

Caflisch

2009

J of Molecular Recognition

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We review our computational tools for high-throughput screening by fragment-based docking of large collections of small molecules. Applications to six different enzymes, four proteases, and two protein kinases, are presented. Remarkably, several low-micromolar inhibitors were discovered in each of the high-throughput docking campaigns. Probable reasons for the lack of submicromolar inhibitors are the tiny fraction of chemical space covered by the libraries of available compounds, as well as the approximations in the methods employed for scoring, and the use of a rigid conformation of the target protein.

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Section: Liece Binding Energy Evaluationsupporting

confidence: 81%

Section: West Nile Virus Ns3 Protease (Flaviviral Infections)mentioning

confidence: 99%

Library screening by fragment‐based docking

Huang

Caflisch

2009

J of Molecular Recognition

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“…Several efforts to find inhibitors for different flavivirus proteases (West Nile virus [WNV], dengue, and yellow fever virus [YFV]) have been reported, with several studies focusing on peptidic substrate-based inhibitors [12][13][14][15][16][17]. Nonpeptidic inhibitors have been identified by in vitro screening [18][19][20] or in silico throughput docking [21]. Most of these compounds do not possess the appropriate properties for drug development, either because the scaffold is too labile [15][16][17]19] or because the inhibitors bind too weakly [18,20].…”

Section: B S T R a C Tmentioning

confidence: 99%

A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease

Bodenreider

Beer

Keller

et al. 2009

Analytical Biochemistry

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In drug discovery, the occurrence of false positives is a major hurdle in the search for lead compounds that can be developed into drugs. A small-molecular-weight compound that inhibits dengue virus protease at low micromolar levels was identified in a screening campaign. Binding to the enzyme was confirmed by isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR). However, a structure-activity relationship study that ensued did not yield more potent leads. To further characterize the parental compound and its analogues, we developed a high-speed, low-cost, quantitative fluorescence quenching assay. We observed that specific analogues quenched dengue protease fluorescence and showed variation in IC (50) values. In contrast, nonspecifically binding compounds did not quench its fluorescence and showed similar IC(50) values with steep dose-response curves. We validated the assay using single Trp-to-Ala protease mutants and the competitive protease inhibitor aprotinin. Specific compounds detected in the binding assay were further analyzed by competitive ITC, NMR, and surface plasmon resonance, and the assay's utility in comparison with these biophysical methods is discussed. The sensitivity of this assay makes it highly useful for hit finding and validation in drug discovery. Furthermore, the technique can be readily adapted for studying other protein-ligand interactions. b s t r a c tIn drug discovery, the occurrence of false positives is a major hurdle in the search for lead compounds that can be developed into drugs. A small-molecular-weight compound that inhibits dengue virus protease at low micromolar levels was identified in a screening campaign. Binding to the enzyme was confirmed by isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR). However, a structure-activity relationship study that ensued did not yield more potent leads. To further characterize the parental compound and its analogues, we developed a high-speed, low-cost, quantitative fluorescence quenching assay. We observed that specific analogues quenched dengue protease fluorescence and showed variation in IC 50 values. In contrast, nonspecifically binding compounds did not quench its fluorescence and showed similar IC 50 values with steep dose-response curves. We validated the assay using single Trp-to-Ala protease mutants and the competitive protease inhibitor aprotinin. Specific compounds detected in the binding assay were further analyzed by competitive ITC, NMR, and surface plasmon resonance, and the assay's utility in comparison with these biophysical methods is discussed. The sensitivity of this assay makes it highly useful for hit finding and validation in drug discovery. Furthermore, the technique can be readily adapted for studying other proteinligand interactions. Ó 2009 Elsevier Inc. All rights reserved.High-throughput screening (HTS) 2 is a major method in drug discovery for new small lead molecules. In high-throughput enzyme inhibition assays, more than a million compounds are usua...

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“…(3)-over the complete test set of 214 complexes with structurally diverse ligands and covering 62 different proteins-is also reasonable compared to the very good 1.0 kcal mol 21 and 0.6 values that have been obtained using the CHARMm force field in several distinct studies using the original LIECE equation. Indeed, in these studies, the LIECE equation was systematically refitted for each set of structurally related molecules binding only to b-secretase, 38,39 HIV-1 protease, 38 plasmepsin, 52 West Nile virus NS3 protease, 53 or different kinases, 40,54 as the subsequent applications were related only to one of these proteins. It is actually expected that, thanks to cancellation of errors, it is easier to find correlations applying only to one protein and a series of related ligands than for unrelated ligands of different proteins.…”

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confidence: 99%

SwissParam: A fast force field generation tool for small organic molecules

et al. 2011

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The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand-protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol(-1), and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer-aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch.

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Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking

Cited by 72 publications

References 62 publications

Library screening by fragment‐based docking

Library screening by fragment‐based docking

A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease

SwissParam: A fast force field generation tool for small organic molecules

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