528
Views
45
CrossRef citations to date
0
Altmetric
Reviews

A structural biology view of target drugability

, PhD & , PhD
Pages 391-401 | Published online: 26 Mar 2008

Bibliography

  • Bains W. Failure rates in drug discovery and development: will we ever get any better? Drug Discov World 2004:9-18
  • Drews J. Research & development. Basic science and pharmaceutical innovation. Nat Biotechnol 1999;17(5):406
  • Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov 2002;1(9):727-30
  • Imming P, Sinning C, Meyer A. Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov 2006;5(10):821-34
  • Wishart DS, Knox C, Guo AC, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006;34(Database issue):D668-72
  • Zheng CJ, Han LY, Yap CW, et al. Therapeutic targets: progress of their exploration and investigation of their characteristics. Pharmacol Rev 2006;58(2):259-79
  • Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there? Nat Rev Drug Discov 2006;5(12):993-6
  • Chen X, Ji ZL, Chen YZ. TTD: Therapeutic Target Database. Nucleic Acids Res 2002;30(1):412-5
  • Paolini GV, Shapland RH, van Hoorn WP, et al. Global mapping of pharmacological space. Nat Biotechnol 2006;24(7):805-15
  • Russ AP, Lampel S. The druggable genome: an update. Drug Discov Today 2005;10(23-24):1607-10
  • Sakharkar MK, Sakharkar KR, Pervaiz S. Druggability of human disease genes. Int J Biochem Cell Biol 2007;39(6):1156-64
  • Lipinski CA. Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 2000;44(1):235-49
  • Han LY, Zheng CJ, Xie B, et al. Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness. Drug Discov Today 2007;12(7-8):304-13
  • Hopkins AL, Groom CR. Target analysis: a priori assessment of druggability. Ernst Schering Res Found Workshop 2003;(42):11-7
  • Keller TH, Pichota A, Yin Z. A practical view of ‘druggability’. Curr Opin Chem Biol 2006;10(4):357-61
  • Zheng C, Han L, Yap CW, et al. Progress and problems in the exploration of therapeutic targets. Drug Discov Today 2006;11(9-10):412-20
  • Meisner NC, Hintersteiner M, Uhl V, et al. The chemical hunt for the identification of drugable targets. Curr Opin Chem Biol 2004;8(4):424-31
  • Egner U, Kratzschmar J, Kreft B, et al. The target discovery process. Chembiochem 2005;6(3):468-79
  • Hajduk PJ, Huth JR, Tse C. Predicting protein druggability. Drug Discov Today 2005;10(23-24):1675-82
  • Leach AR, Hann MM, Burrows JN, Griffen EJ. Fragment screening: an introduction. Mol Biosyst 2006;2(9):430-46
  • Schade M. NMR fragment screening: advantages and applications. IDrugs 2006;9(2):110-3
  • Schuffenhauer A, Ruedisser S, Marzinzik AL, et al. Library design for fragment based screening. Curr Top Med Chem 2005;5(8):751-62
  • Hajduk PJ, Huth JR, Fesik SW. Druggability indices for protein targets derived from NMR-based screening data. J Med Chem 2005;48(7):2518-25
  • Yuan Z, Burrage K, Mattick JS. Prediction of protein solvent accessibility using support vector machines. Proteins 2002;48(3):566-70
  • Hasan S, Daugelat S, Rao PS, Schreiber M. Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis. PLoS Comput Biol 2006;2(6):e61
  • Li H, Gao Z, Kang L, et al. TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res 2006;34(Web Server issue):W219-24
  • Hambly K, Danzer J, Muskal S, Debe DA. Interrogating the druggable genome with structural informatics. Mol Divers 2006;10(3):273-81
  • Finn RD, Mistry J, Schuster-Bockler B, et al. Pfam: clans, web tools and services. Nucleic Acids Res 2006;34(Database issue):D247-51
  • Chuaqui C, Deng Z, Singh J. Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. J Med Chem 2005;48(1):121-33
  • Deng Z, Chuaqui C, Singh J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem 2004;47(2):337-44
  • Sheinerman FB, Giraud E, Laoui A. High affinity targets of protein kinase inhibitors have similar residues at the positions energetically important for binding. J Mol Biol 2005;352(5):1134-56
  • Vajda S, Guarnieri F. Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel 2006;9(3):354-62
  • Berman HM, Bhat TN, Bourne PE, et al. The Protein Data Bank and the challenge of structural genomics. Nat Struct Biol 2000;7(Suppl):957-9
  • Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res 2000;28(1):235-42
  • Mestres J. Representativity of target families in the Protein Data Bank: impact for family-directed structure-based drug discovery. Drug Discov Today 2005;10(23-24):1629-37
  • Holler TP, Evdokimov AG, Narasimhan L. Structural Biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2007;2(8):1085-101
  • Sinnecker S, Neese F. QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study. J Comput Chem 2006;27(12):1463-75
  • Villar R, Gil MJ, Garcia JI, Martinez-Merino V. Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs? J Comput Chem 2005;26(13):1347-58
  • Laurie AT, Jackson RM. Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci 2006;7(5):395-406
  • Nayal M, Honig B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins 2006;63(4):892-906
  • Bergner A, Günther J. Structural aspects of binding site similarity: a 3D upgrade for chemogenomics: WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim; 2004
  • An J, Totrov M, Abagyan R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics 2005;4(6):752-61
  • Glaser F, Morris RJ, Najmanovich RJ, et al. A method for localizing ligand binding pockets in protein structures. Proteins 2006;62(2):479-88
  • Halgren T. New method for fast and accurate binding-site identification and analysis. Chem Biol Drug Des 2007;69(2):146-8
  • Kellenberger E, Muller P, Schalon C, et al. sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. J Chem Inf Model 2006;46(2):717-27
  • Golovin A, Dimitropoulos D, Oldfield T, et al. MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites. Proteins 2005;58(1):190-9
  • Kinoshita K, Nakamura H. Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci 2005;14(3):711-8
  • Brown SP, Hajduk PJ. Effects of conformational dynamics on predicted protein druggability. ChemMedChem 2006;1(1):70-2
  • Eyrisch S, Helms V. Transient pockets on protein surfaces involved in protein-protein interaction. J Med Chem 2007;50(15):3457-64
  • Cheng AC, Coleman RG, Smyth KT, et al. Structure-based maximal affinity model predicts small-molecule druggability. Nat Biotechnol 2007;25(1):71-5
  • Coleman RG, Salzberg AC, Cheng AC. Structure-based identification of small molecule binding sites using a free energy model. J Chem Inf Model 2006;46(6):2631-7
  • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Del Rev 2001;46(1-3):3-26
  • Fauman EB, Hopkins AL, Groom CR. Structural bioinformatics in drug discovery. Methods Biochem Anal 2003;44:477-97
  • Proudfoot JR. The evolution of synthetic oral drug properties. Bioorg Med Chem Lett 2005;15(4):1087-90
  • Folkertsma S, van Noort PI, Brandt RF, et al. The nuclear receptor ligand-binding domain: a family-based structure analysis. Curr Med Chem 2005;12(9):1001-16
  • Mochalkin I, Lightle S, Narasimhan L, et al. Structure of a small-molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site. Protein Sci 2008;17(3):577-82
  • Todd AE, Orengo CA, Thornton JM. Plasticity of enzyme active sites. Trends Biochem Sci 2002;27(8):419-26
  • Schäfer M, Egner U. Structural aspects of drugability and selectivity of protein kinases in inflammation. Anti Inflamm Anti Allergy Agents Med Chem 2007;6:5-17
  • Ahmad T, Eisen T. Kinase inhibition with BAY 43-9006 in renal cell carcinoma. Clin Cancer Res 2004;10(18 Pt 2):S6388-92
  • Kallen J, Lattmann R, Beerli R, et al. Crystal structure of human estrogen-related receptor {alpha} in complex with a synthetic inverse agonist reveals its novel molecular mechanism. J Biol Chem 2007;282(32):23231-9
  • Dudkina AS, Lindsley CW. Small molecule protein-protein inhibitors for the p53-MDM2 interaction. Curr Top Med Chem 2007;7(10):952-60
  • Adler M, Kochanny MJ, Ye B, et al. Crystal structures of two potent nonamidine inhibitors bound to factor Xa. Biochemistry 2002;41(52):15514-23
  • Lucking U, Siemeister G, Schafer M, et al. Macrocyclic aminopyrimidines as multitarget CDK and VEGF-R inhibitors with potent antiproliferative activities. ChemMedChem 2007;2(1):63-77
  • Vassilev LT, Vu BT, Graves B, et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 2004;303(5659):844-8
  • Song H, Hanlon N, Brown NR, et al. Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2. Mol Cell 2001;7(3):615-26
  • Wan PT, Garnett MJ, Roe SM, et al. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 2004;116(6):855-67
  • Shewchuk LM, Hassell AM, Ellis B, et al. Structure of the Tie2 RTK domain: self-inhibition by the nucleotide binding loop, activation loop, and C-terminal tail. Structure 2000;8(11):1105-13

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.