51
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Su XC, Ozawa K, Yagi H, Lim SP, Wen D, Ekonomiuk D, Huang D, Keller TH, Sonntag S, Caflisch A, Vasudevan SG, Otting G. NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS J 2009; 276:4244-55. [PMID: 19583774 DOI: 10.1111/j.1742-4658.2009.07132.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The two-component NS2B-NS3 protease of West Nile virus is essential for its replication and presents an attractive target for drug development. Here, we describe protocols for the high-yield expression of stable isotope-labelled samples in vivo and in vitro. We also describe the use of NMR spectroscopy to determine the binding mode of new low molecular mass inhibitors of the West Nile virus NS2B-NS3 protease which were discovered using high-throughput in vitro screening. Binding to the substrate-binding sites S1 and S3 is confirmed by intermolecular NOEs and comparison with the binding mode of a previously identified low molecular mass inhibitor. Our results show that all these inhibitors act by occupying the substrate-binding site of the protease rather than by an allosteric mechanism. In addition, the NS2B polypeptide chain was found to be positioned near the substrate-binding site, as observed previously in crystal structures of the protease in complex with peptide inhibitors or bovine pancreatic trypsin inhibitor. This indicates that the new low molecular mass compounds, although inhibiting the protease, also promote the proteolytically active conformation of NS2B, which is very different from the crystal structure of the protein without inhibitor.
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Affiliation(s)
- Xun-Cheng Su
- Research School of Chemistry, Australian National University, Canberra, Australia
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52
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Friedman R, Caflisch A. Discovery of Plasmepsin Inhibitors by Fragment-Based Docking and Consensus Scoring. ChemMedChem 2009; 4:1317-26. [DOI: 10.1002/cmdc.200900078] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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53
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Hamada Y, Kiso Y. Recent progress in the drug discovery of non-peptidic BACE1 inhibitors. Expert Opin Drug Discov 2009; 4:391-416. [DOI: 10.1517/17460440902806377] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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54
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Gianti E, Sartori L. Identification and selection of "privileged fragments" suitable for primary screening. J Chem Inf Model 2009; 48:2129-39. [PMID: 18991373 DOI: 10.1021/ci800219h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of small molecule libraries for fragment-based primary screening (FBS) is a well-known approach to identify protein binders in the low affinity range. However, the search, analysis, and selection of suitable screening fragments can be a lengthy process, because of the large number of compounds that must be analyzed for different levels of ring/substituents identification and submitted to selection/exclusion criteria based on their physicochemical properties. The purpose of the present work is to propose a strategy to identify substructures from databases of known drugs, which can be used as templates for the generation of libraries of "privileged fragments" that are able to provide high-quality hits. The entire process has been developed integrating Pipeline Pilot (Accelrys Inc., San Diego, CA; http://www.accelrys.com ) native components and user-defined molecular files containing ISIS-like substructure query features (Symyx, San Ramon, CA; http://www.symyx.com ). The method is effortless, easy to put in place, and fast enough to be iteratively applied to different sources of druglike compounds.
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Affiliation(s)
- Eleonora Gianti
- Computational Sciences Group, Department of Chemistry (Congenia s.r.l.), Genextra S.p.A., Milan MI 20100, Italy
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55
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Kolb P, Kipouros CB, Huang D, Caflisch A. Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors. Proteins 2009; 73:11-8. [PMID: 18384152 DOI: 10.1002/prot.22028] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
High-throughput docking is a computational tool frequently used to discover small-molecule inhibitors of enzymes or receptors of known three-dimensional structure. Because of the large number of molecules in chemical libraries, automatic procedures to prune multimillion compound collections are useful for high-throughput docking and necessary for in vitro screening. Here, we propose an anchor-based library tailoring approach (termed ALTA) to focus a chemical library by docking and prioritizing molecular fragments according to their binding energy which includes continuum electrostatics solvation. In principle, ALTA does not require prior knowledge of known inhibitors, but receptor-based pharmacophore information (hydrogen bonds with the hinge region) is additionally used here to identify molecules with optimal anchor fragments for the ATP-binding site of the EphB4 receptor tyrosine kinase. The 21,418 molecules of the focused library (from an initial collection of about 730,000) are docked into EphB4 and ranked by force-field-based energy including electrostatic solvation. Among the 43 compounds tested in vitro, eight molecules originating from two different anchors show low-micromolar activity in a fluorescence-based enzymatic assay. Four of them are active in a cell-based assay and are potential anti-angiogenic compounds.
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Affiliation(s)
- Peter Kolb
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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56
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Zoete V, Grosdidier A, Michielin O. Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med 2009; 13:238-48. [PMID: 19183238 PMCID: PMC3823351 DOI: 10.1111/j.1582-4934.2008.00665.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The drug discovery process has been profoundly changed recently by the adoption of computational methods helping the design of new drug candidates more rapidly and at lower costs. In silico drug design consists of a collection of tools helping to make rational decisions at the different steps of the drug discovery process, such as the identification of a biomolecular target of therapeutical interest, the selection or the design of new lead compounds and their modification to obtain better affinities, as well as pharmacokinetic and pharmacodynamic properties. Among the different tools available, a particular emphasis is placed in this review on molecular docking, virtual high-throughput screening and fragment-based ligand design.
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Affiliation(s)
- Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, Quartier Sorge, Lausanne, Switzerland
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57
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Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Negl Trop Dis 2009; 3:e356. [PMID: 19159012 PMCID: PMC2613028 DOI: 10.1371/journal.pntd.0000356] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 12/14/2008] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The non-structural 3 protease (NS3pro) is an essential flaviviral enzyme and therefore one of the most promising targets for drug development against West Nile virus (WNV) and dengue infections. METHODOLOGY In this work, a small-molecule inhibitor of the WNV NS3pro has been identified by automatic fragment-based docking of about 12000 compounds and testing by nuclear magnetic resonance (NMR) spectroscopy of only 22 molecules. Specific binding of the inhibitor into the active site of NS3pro and its binding mode are confirmed by 15N-HSQC NMR spectra. The inhibitory activity is further validated by an enzymatic assay and a tryptophan fluorescence quenching assay. CONCLUSION The inhibitor [4-(carbamimidoylsulfanylmethyl)-2,5-dimethylphenyl]-methylsulfanylmethanimidamide has a good ratio of binding affinity versus molecular weight (ligand efficiency of 0.33 kcal/mol per non-hydrogen atom), and thus has good potential as lead compound for further development to combat West Nile virus infections.
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58
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59
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Schenker P, Alfarano P, Kolb P, Caflisch A, Baici A. A double-headed cathepsin B inhibitor devoid of warhead. Protein Sci 2008; 17:2145-55. [PMID: 18796695 DOI: 10.1110/ps.037341.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Most synthetic inhibitors of peptidases have been targeted to the active site for inhibiting catalysis through reversible competition with the substrate or by covalent modification of catalytic groups. Cathepsin B is unique among the cysteine peptidase for the presence of a flexible segment, known as the occluding loop, which can block the primed subsites of the substrate binding cleft. With the occluding loop in the open conformation cathepsin B acts as an endopeptidase, and it acts as an exopeptidase when the loop is closed. We have targeted the occluding loop of human cathepsin B at its surface, outside the catalytic center, using a high-throughput docking procedure. The aim was to identify inhibitors that would interact with the occluding loop thereby modulating enzyme activity without the help of chemical warheads against catalytic residues. From a large library of compounds, the in silico approach identified [2-[2-(2,4-dioxo-1,3-thiazolidin-3-yl)ethylamino]-2-oxoethyl] 2-(furan-2-carbonylamino) acetate, which fulfills the working hypothesis. This molecule possesses two distinct binding moieties and behaves as a reversible, double-headed competitive inhibitor of cathepsin B by excluding synthetic and protein substrates from the active center. The kinetic mechanism of inhibition suggests that the occluding loop is stabilized in its closed conformation, mainly by hydrogen bonds with the inhibitor, thus decreasing endoproteolytic activity of the enzyme. Furthermore, the dioxothiazolidine head of the compound sterically hinders binding of the C-terminal residue of substrates resulting in inhibition of the exopeptidase activity of cathepsin B in a physiopathologically relevant pH range.
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Affiliation(s)
- Patricia Schenker
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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60
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Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol 2008; 153 Suppl 1:S7-26. [PMID: 18037925 PMCID: PMC2268060 DOI: 10.1038/sj.bjp.0707515] [Citation(s) in RCA: 316] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 09/18/2007] [Accepted: 09/24/2007] [Indexed: 11/08/2022] Open
Abstract
Accelerating the drug discovery process requires predictive computational protocols capable of reducing or simplifying the synthetic and/or combinatorial challenge. Docking-based virtual screening methods have been developed and successfully applied to a number of pharmaceutical targets. In this review, we first present the current status of docking and scoring methods, with exhaustive lists of these. We next discuss reported comparative studies, outlining criteria for their interpretation. In the final section, we describe some of the remaining developments that would potentially lead to a universally applicable docking/scoring method.
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Affiliation(s)
- N Moitessier
- Department of Chemistry, McGill University, Montréal, Québec, Canada.
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61
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Dey F, Caflisch A. Fragment-based de novo ligand design by multiobjective evolutionary optimization. J Chem Inf Model 2008; 48:679-90. [PMID: 18307332 DOI: 10.1021/ci700424b] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GANDI (Genetic Algorithm-based de Novo Design of Inhibitors) is a computational tool for automatic fragment-based design of molecules within a protein binding site of known structure. A genetic algorithm and a tabu search act in concert to join predocked fragments with a user-supplied list of fragments. A novel feature of GANDI is the simultaneous optimization of force field energy and a term enforcing 2D-similarity to known inhibitor(s) or 3D-overlap to known binding mode(s). Scaffold hopping can be promoted by tuning the relative weights of these terms. The performance of GANDI is tested on cyclin-dependent kinase 2 (CDK2) using a library of about 14 000 fragments and the binding mode of a known oxindole inhibitor to bias the design. Top ranking GANDI molecules are involved in one to three hydrogen bonds with the backbone polar groups in the hinge region of CDK2, an interaction pattern observed in potent kinase inhibitors. Notably, a GANDI molecule with very favorable predicted binding affinity shares a 2-N-phenyl-1,3-thiazole-2,4-diamine moiety with a known nanomolar inhibitor of CDK2. Importantly, molecules with a favorable GANDI score are synthetic accessible. In fact, eight of the 1809 molecules designed by GANDI for CDK2 are found in the ZINC database of commercially available compounds which also contains about 600 compounds with identical scaffolds as those in the top ranking GANDI molecules.
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Affiliation(s)
- Fabian Dey
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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62
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Kolb P, Huang D, Dey F, Caflisch A. Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model. J Med Chem 2008; 51:1179-88. [DOI: 10.1021/jm070654j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Peter Kolb
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Danzhi Huang
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Dey
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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