The Role of Protein Structural Analysis in the Next Generation Sequencing Era

Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 336)


Proteins are macromolecules that serve a cell’s myriad processes and functions in all living organisms via dynamic interactions with other proteins, small molecules and cellular components. Genetic variations in the protein-encoding regions of the human genome account for >85% of all known Mendelian diseases, and play an influential role in shaping complex polygenic diseases. Proteins also serve as the predominant target class for the design of small molecule drugs to modulate their activity. Knowledge of the shape and form of proteins, by means of their three-dimensional structures, is therefore instrumental to understanding their roles in disease and their potentials for drug development. In this chapter we outline, with the wide readership of non-structural biologists in mind, the various experimental and computational methods available for protein structure determination. We summarize how the wealth of structure information, contributed to a large extent by the technological advances in structure determination to date, serves as a useful tool to decipher the molecular basis of genetic variations for disease characterization and diagnosis, particularly in the emerging era of genomic medicine, and becomes an integral component in the modern day approach towards rational drug development.


Drug development Genetic diseases Misfolding Missense mutations Mutation analysis Protein structures Structure based drug design 


  1. 1.
    Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC (1958) A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181(4610):662–666Google Scholar
  2. 2.
    Savitsky P, Bray J, Cooper CD, Marsden BD, Mahajan P, Burgess-Brown NA et al (2010) High-throughput production of human proteins for crystallization: the SGC experience. J Struct Biol 172(1):3–13Google Scholar
  3. 3.
    Page R, Stevens RC (2004) Crystallization data mining in structural genomics: using positive and negative results to optimize protein crystallization screens. Methods 34(3):373–389Google Scholar
  4. 4.
    Joachimiak A (2009) High-throughput crystallography for structural genomics. Curr Opin Struct Biol 19(5):573–584Google Scholar
  5. 5.
    Manjasetty BA, Turnbull AP, Panjikar S, Bussow K, Chance MR (2008) Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. Proteomics 8(4):612–625Google Scholar
  6. 6.
    Pellecchia M, Sem DS, Wuthrich K (2002) NMR in drug discovery. Nat Rev Drug Discov 1(3):211–219Google Scholar
  7. 7.
    Billeter M, Wagner G, Wuthrich K (2008) Solution NMR structure determination of proteins revisited. J Biomol NMR 42(3):155–158Google Scholar
  8. 8.
    Frank J (2002) Single-particle imaging of macromolecules by cryo-electron microscopy. Annu Rev Biophys Biomol Struct 31:303–319Google Scholar
  9. 9.
    Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325Google Scholar
  10. 10.
    Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823–826Google Scholar
  11. 11.
    Cavasotto CN, Phatak SS (2009) Homology modeling in drug discovery: current trends and applications. Drug Discov Today 14(13–14):676–683Google Scholar
  12. 12.
    Yue P, Li Z, Moult J (2005) Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 353(2):459–473Google Scholar
  13. 13.
    Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E et al (2004) The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat 23(5):464–470Google Scholar
  14. 14.
    Tramontano A, Morea V (2003) Assessment of homology-based predictions in CASP5. Proteins 53(Suppl 6):352–368Google Scholar
  15. 15.
    Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11(1):31–46Google Scholar
  16. 16.
    Ng SB, Nickerson DA, Bamshad MJ, Shendure J (2010) Massively parallel sequencing and rare disease. Hum Mol Genet 19(R2):R119–R124Google Scholar
  17. 17.
    Ku CS, Naidoo N, Pawitan Y (2011) Revisiting Mendelian disorders through exome sequencing. Hum Genet 129(4):351–370Google Scholar
  18. 18.
    Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM et al (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42(1):30–35Google Scholar
  19. 19.
    Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C et al (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461(7261):272–276Google Scholar
  20. 20.
    Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI et al (2010) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42(9):790–793Google Scholar
  21. 21.
    International HapMap Consortium (2003) The International HapMap Project. Nature 426(6968):789–796Google Scholar
  22. 22.
    Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33(Database issue):D514–D517Google Scholar
  23. 23.
    Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS et al (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat 21(6):577–581Google Scholar
  24. 24.
    Thusberg J, Vihinen M (2009) Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. Hum Mutat 30(5):703–714Google Scholar
  25. 25.
    Jordan DM, Ramensky VE, Sunyaev SR (2010) Human allelic variation: perspective from protein function, structure, and evolution. Curr Opin Struct Biol 20(3):342–350Google Scholar
  26. 26.
    Karchin R (2009) Next generation tools for the annotation of human SNPs. Brief Bioinform 10(1):35–52Google Scholar
  27. 27.
    Sunyaev S, Ramensky V, Bork P (2000) Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet 16(5):198–200Google Scholar
  28. 28.
    Miller MP, Kumar S (2001) Understanding human disease mutations through the use of interspecific genetic variation. Hum Mol Genet 10(21):2319–2328Google Scholar
  29. 29.
    Hicks S, Wheeler DA, Plon SE, Kimmel M (2011) Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat 32(6):661–668Google Scholar
  30. 30.
    Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R (2009) Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat 30(8):1237–1244Google Scholar
  31. 31.
    Yue P, Moult J (2006) Identification and analysis of deleterious human SNPs. J Mol Biol 356(5):1263–1274Google Scholar
  32. 32.
    Lobo PA, Van Petegem F (2009) Crystal structures of the N-terminal domains of cardiac and skeletal muscle ryanodine receptors: insights into disease mutations. Structure 17(11):1505–1514Google Scholar
  33. 33.
    Lew ED, Bae JH, Rohmann E, Wollnik B, Schlessinger J (2007) Structural basis for reduced FGFR2 activity in LADD syndrome: implications for FGFR autoinhibition and activation. Proc Natl Acad Sci USA 104(50):19802–19807Google Scholar
  34. 34.
    Chaikuad A, Froese DS, Berridge G, von Delft F, Oppermann U, Yue WW (2011) Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis. Proc Natl Acad Sci USA 108(52):21028–21033Google Scholar
  35. 35.
    Malay AD, Procious SL, Tolan DR (2002) The temperature dependence of activity and structure for the most prevalent mutant aldolase B associated with hereditary fructose intolerance. Arch Biochem Biophys 408(2):295–304Google Scholar
  36. 36.
    Zhang Z, Norris J, Schwartz C, Alexov E (2011) In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase. PLoS One 6(5):e20373Google Scholar
  37. 37.
    Anderson PC, Daggett V (2008) Molecular basis for the structural instability of human DJ-1 induced by the L166P mutation associated with Parkinson’s disease. Biochemistry 47(36):9380–9393Google Scholar
  38. 38.
    Niesen FH, Berglund H, Vedadi M (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2(9):2212–2221Google Scholar
  39. 39.
    Froese DS, Kochan G, Muniz JR, Wu X, Gileadi C, Ugochukwu E et al (2010) Structures of the human GTPase MMAA and vitamin B12-dependent methylmalonyl-CoA mutase and insight into their complex formation. J Biol Chem 285(49):38204–38213Google Scholar
  40. 40.
    Wu L, Pan L, Wei Z, Zhang M (2011) Structure of MyTH4-FERM domains in myosin VIIa tail bound to cargo. Science 331(6018):757–760Google Scholar
  41. 41.
    Bridwell-Rabb J, Winn AM, Barondeau DP (2011) Structure-function analysis of Friedreich’s ataxia mutants reveals determinants of frataxin binding and activation of the Fe-S assembly complex. Biochemistry 50(33):7265–7274Google Scholar
  42. 42.
    Wang Z, Moult J (2001) SNPs, protein structure, and disease. Hum Mutat 17(4):263–270Google Scholar
  43. 43.
    Gregersen N, Bross P, Vang S, Christensen JH (2006) Protein misfolding and human disease. Annu Rev Genomics Hum Genet 7:103–124Google Scholar
  44. 44.
    Mitchell JJ, Trakadis YJ, Scriver CR (2011) Phenylalanine hydroxylase deficiency. Genet Med 13(8):697–707Google Scholar
  45. 45.
    Dobson CM (2004) Principles of protein folding, misfolding and aggregation. Semin Cell Dev Biol 15(1):3–16Google Scholar
  46. 46.
    Jennings IG, Cotton RG, Kobe B (2000) Structural interpretation of mutations in phenylalanine hydroxylase protein aids in identifying genotype-phenotype correlations in phenylketonuria. Eur J Hum Genet 8(9):683–696Google Scholar
  47. 47.
    Erlandsen H, Stevens RC (1999) The structural basis of phenylketonuria. Mol Genet Metab 68(2):103–125Google Scholar
  48. 48.
    Dobrowolski SF, Pey AL, Koch R, Levy H, Ellingson CC, Naylor EW et al (2009) Biochemical characterization of mutant phenylalanine hydroxylase enzymes and correlation with clinical presentation in hyperphenylalaninaemic patients. J Inherit Metab Dis 32(1):10–21Google Scholar
  49. 49.
    Pey AL, Stricher F, Serrano L, Martinez A (2007) Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet 81(5):1006–1024Google Scholar
  50. 50.
    Gersting SW, Kemter KF, Staudigl M, Messing DD, Danecka MK, Lagler FB et al (2008) Loss of function in phenylketonuria is caused by impaired molecular motions and conformational instability. Am J Hum Genet 83(1):5–17Google Scholar
  51. 51.
    Matthews BW (1993) Structural and genetic analysis of protein stability. Annu Rev Biochem 62:139–160Google Scholar
  52. 52.
    Xiao J, Madhan B, Li Y, Brodsky B, Baum J (2011) Osteogenesis imperfecta model peptides: incorporation of residues replacing Gly within a triple helix achieved by renucleation and local flexibility. Biophys J 101(2):449–458Google Scholar
  53. 53.
    Tang NL, Hui J, Young E, Worthington V, To KF, Cheung KL et al (2003) A novel mutation (G233D) in the glycogen phosphorylase gene in a patient with hepatic glycogen storage disease and residual enzyme activity. Mol Genet Metab 79(2):142–145Google Scholar
  54. 54.
    Wu WW, Molday RS (2003) Defective discoidin domain structure, subunit assembly, and endoplasmic reticulum processing of retinoschisin are primary mechanisms responsible for X-linked retinoschisis. J Biol Chem 278(30):28139–28146Google Scholar
  55. 55.
    Malay AD, Allen KN, Tolan DR (2005) Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance. J Mol Biol 347(1):135–144Google Scholar
  56. 56.
    Jeyabalan J, Nesbit MA, Galvanovskis J, Callaghan R, Rorsman P, Thakker RV (2010) SEDLIN forms homodimers: characterisation of SEDLIN mutations and their interactions with transcription factors MBP1, PITX1 and SF1. PLoS One 5(5):e10646Google Scholar
  57. 57.
    Joerger AC, Fersht AR (2007) Structural biology of the tumor suppressor p53 and cancer-associated mutants. Adv Cancer Res 97:1–23Google Scholar
  58. 58.
    Cho Y, Gorina S, Jeffrey PD, Pavletich NP (1994) Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 265(5170):346–355Google Scholar
  59. 59.
    Amador FJ, Liu S, Ishiyama N, Plevin MJ, Wilson A, MacLennan DH et al (2009) Crystal structure of type I ryanodine receptor amino-terminal beta-trefoil domain reveals a disease-associated mutation “hot spot” loop. Proc Natl Acad Sci USA 106(27):11040–11044Google Scholar
  60. 60.
    Li S, Duan J, Li D, Yang B, Dong M, Ye K (2011) Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase. Genes Dev 25(22):2409–2421Google Scholar
  61. 61.
    Picaud S, Kavanagh KL, Yue WW, Lee WH, Muller-Knapp S, Gileadi O et al (2011) Structural basis of fumarate hydratase deficiency. J Inherit Metab Dis 34(3):671–676Google Scholar
  62. 62.
    Lee WH, Yue WW, Raush E, Totrov M, Abagyan R, Oppermann U et al (2011) Interactive JIMD articles using the iSee concept: turning a new page on structural biology data. J Inherit Metab Dis 34(3):565–567Google Scholar
  63. 63.
    Lahiry P, Torkamani A, Schork NJ, Hegele RA (2010) Kinase mutations in human disease: interpreting genotype-phenotype relationships. Nat Rev Genet 11(1):60–74Google Scholar
  64. 64.
    Gong S, Blundell TL (2010) Structural and functional restraints on the occurrence of single amino acid variations in human proteins. PLoS One 5(2):e9186Google Scholar
  65. 65.
    Hurst JM, McMillan LE, Porter CT, Allen J, Fakorede A, Martin AC (2009) The SAAPdb web resource: a large-scale structural analysis of mutant proteins. Hum Mutat 30(4):616–624Google Scholar
  66. 66.
    Khan S, Vihinen M (2007) Spectrum of disease-causing mutations in protein secondary structures. BMC Struct Biol 7:56Google Scholar
  67. 67.
    Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1(9):727–730Google Scholar
  68. 68.
    Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev Drug Discov 5(12):993–996Google Scholar
  69. 69.
    Imming P, Sinning C, Meyer A (2006) Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov 5(10):821–834Google Scholar
  70. 70.
    Rask-Andersen M, Almen MS, Schioth HB (2011) Trends in the exploitation of novel drug targets. Nat Rev Drug Discov 10(8):579–590Google Scholar
  71. 71.
    Morgan S, Grootendorst P, Lexchin J, Cunningham C, Greyson D (2011) The cost of drug development: a systematic review. Health Policy 100(1):4–17Google Scholar
  72. 72.
    Paul SM, Mytelka DS, Dunwiddie CT, Persinger CC, Munos BH, Lindborg SR et al (2010) How to improve R&D productivity: the pharmaceutical industry’s grand challenge. Nat Rev Drug Discov 9(3):203–214. doi:10.1038/nrd3078 Google Scholar
  73. 73.
    Hassall CH, Krohn A, Moody CJ, Thomas WA (1982) The design of a new group of angiotensin-converting enzyme inhibitors. FEBS Lett 147(2):175–179Google Scholar
  74. 74.
    Lapatto R, Blundell T, Hemmings A, Overington J, Wilderspin A, Wood S et al (1989) X-Ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Nature 342(6247):299–302Google Scholar
  75. 75.
    Miller M, Schneider J, Sathyanarayana BK, Toth MV, Marshall GR, Clawson L et al (1989) Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Science 246(4934):1149–1152Google Scholar
  76. 76.
    Supuran CT, Scozzafava A, Casini A (2003) Carbonic anhydrase inhibitors. Med Res Rev 23(2):146–189Google Scholar
  77. 77.
    von Itzstein M, Wu W-Y, Kok GB, Pegg MS, Dyason JC, Jin B et al (1993) Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 363(6428):418–423. doi:10.1038/363418a0 Google Scholar
  78. 78.
    Lew W, Chen X, Kim CU (2000) Discovery and development of GS 4104 (oseltamivir) an orally active influenza neuraminidase inhibitor. Curr Med Chem 7(6):663–672Google Scholar
  79. 79.
    Tokarski JS, Newitt JA, Chang CY, Cheng JD, Wittekind M, Kiefer SE et al (2006) The structure of Dasatinib (BMS-354825) bound to activated ABL kinase domain elucidates its inhibitory activity against imatinib-resistant ABL mutants. Cancer Res 66(11):5790–5797Google Scholar
  80. 80.
    Schindler T, Bornmann W, Pellicena P, Miller WT, Clarkson B, Kuriyan J (2000) Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289(5486):1938–1942Google Scholar
  81. 81.
    Chen L, Jiao ZH, Zheng LS, Zhang YY, Xie ST, Wang ZX et al (2009) Structural insight into the autoinhibition mechanism of AMP-activated protein kinase. Nature 459(7250):1146–1149Google Scholar
  82. 82.
    Yuan P, Bartlam M, Lou Z, Chen S, Zhou J, He X et al (2009) Crystal structure of an avian influenza polymerase PA(N) reveals an endonuclease active site. Nature 458(7240):909–913Google Scholar
  83. 83.
    Williams PA, Cosme J, Vinkovic DM, Ward A, Angove HC, Day PJ et al (2004) Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science 305(5684):683–686Google Scholar
  84. 84.
    Zhang H, Tweel B, Li J, Tong L (2004) Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with CP-640186. Structure 12(9):1683–1691Google Scholar
  85. 85.
    Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R et al (2008) Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454(7203):486–491Google Scholar
  86. 86.
    Cammer SA, Hoffman BT, Speir JA, Canady MA, Nelson MR, Knutson S et al (2003) Structure-based active site profiles for genome analysis and functional family subclassification. J Mol Biol 334(3):387–401Google Scholar
  87. 87.
    Grabowski M, Chruszcz M, Zimmerman MD, Kirillova O, Minor W (2009) Benefits of structural genomics for drug discovery research. Infect Disord Drug Targets 9(5):459–474Google Scholar
  88. 88.
    Shin DH, Hou J, Chandonia JM, Das D, Choi IG, Kim R et al (2007) Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics 8(2–3):99–105Google Scholar
  89. 89.
    Weigelt J (2010) Structural genomics-impact on biomedicine and drug discovery. Exp Cell Res 316(8):1332–1338Google Scholar
  90. 90.
    Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D et al (2009) PSI-2: structural genomics to cover protein domain family space. Structure 17(6):869–881Google Scholar
  91. 91.
    Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R et al (2011) The TB structural genomics consortium: a decade of progress. Tuberculosis (Edinb) 91(2):155–172Google Scholar
  92. 92.
    Ehebauer MT, Wilmanns M (2011) The progress made in determining the Mycobacterium tuberculosis structural proteome. Proteomics 11(15):3128–3133Google Scholar
  93. 93.
    Yue WW, Oppermann U (2011) High-throughput structural biology of metabolic enzymes and its impact on human diseases. J Inherit Metab Dis 34(3):575–581Google Scholar
  94. 94.
    Edwards A (2009) Large-scale structural biology of the human proteome. Annu Rev Biochem 78:541–568Google Scholar
  95. 95.
    Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O et al (2010) Selective inhibition of BET bromodomains. Nature 468(7327):1067–1073Google Scholar
  96. 96.
    Perot S, Sperandio O, Miteva MA, Camproux AC, Villoutreix BO (2010) Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov Today 15(15–16):656–667Google Scholar
  97. 97.
    Hammes-Schiffer S, Benkovic SJ (2006) Relating protein motion to catalysis. Annu Rev Biochem 75:519–541Google Scholar
  98. 98.
    Keller TH, Pichota A, Yin Z (2006) A practical view of ‘druggability’. Curr Opin Chem Biol 10(4):357–361Google Scholar
  99. 99.
    Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46(1–3):3–26Google Scholar
  100. 100.
    Hajduk PJ, Huth JR, Fesik SW (2005) Druggability indices for protein targets derived from NMR-based screening data. J Med Chem 48(7):2518–2525Google Scholar
  101. 101.
    Cheng AC, Coleman RG, Smyth KT, Cao Q, Soulard P, Caffrey DR et al (2007) Structure-based maximal affinity model predicts small-molecule druggability. Nat Biotechnol 25(1):71–75Google Scholar
  102. 102.
    Ciulli A, Williams G, Smith AG, Blundell TL, Abell C (2006) Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods. J Med Chem 49(16):4992–5000Google Scholar
  103. 103.
    Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450(7172):1001–1009. doi:10.1038/nature06526 Google Scholar
  104. 104.
    Bleicher KH, Bohm HJ, Muller K, Alanine AI (2003) Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov 2(5):369–378Google Scholar
  105. 105.
    Macarron R, Banks MN, Bojanic D, Burns DJ, Cirovic DA, Garyantes T et al (2011) Impact of high-throughput screening in biomedical research. Nat Rev Drug Discov 10(3):188–195. doi:10.1038/nrd3368 Google Scholar
  106. 106.
    Klebe G (2006) Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 11(13–14):580–594Google Scholar
  107. 107.
    Kalyaanamoorthy S, Chen YP (2011) Structure-based drug design to augment hit discovery. Drug Discov Today 16(17–18):831–839Google Scholar
  108. 108.
    Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ (2006) In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells. Bioorg Med Chem Lett 16(7):1969–1974Google Scholar
  109. 109.
    Dooley AJ, Shindo N, Taggart B, Park JG, Pang YP (2006) From genome to drug lead: identification of a small-molecule inhibitor of the SARS virus. Bioorg Med Chem Lett 16(4):830–833Google Scholar
  110. 110.
    McLean LR, Zhang Y, Degnen W, Peppard J, Cabel D, Zou C et al (2010) Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures. Bioorg Med Chem Lett 20(6):1981–1984Google Scholar
  111. 111.
    Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ et al (2010) Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem 53(13):4891–4905Google Scholar
  112. 112.
    Schneider G, Hartenfeller M, Reutlinger M, Tanrikulu Y, Proschak E, Schneider P (2009) Voyages to the (un)known: adaptive design of bioactive compounds. Trends Biotechnol 27(1):18–26Google Scholar
  113. 113.
    Hartenfeller M, Schneider G (2011) De novo drug design. Methods Mol Biol 672:299–323Google Scholar
  114. 114.
    Fink T, Bruggesser H, Reymond JL (2005) Virtual exploration of the small-molecule chemical universe below 160 Daltons. Angew Chem Int Ed Engl 44(10):1504–1508Google Scholar
  115. 115.
    Heikkila T, Thirumalairajan S, Davies M, Parsons MR, McConkey AG, Fishwick CW et al (2006) The first de novo designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. Bioorg Med Chem Lett 16(1):88–92Google Scholar
  116. 116.
    Ni S, Yuan Y, Huang J, Mao X, Lv M, Zhu J et al (2009) Discovering potent small molecule inhibitors of cyclophilin A using de novo drug design approach. J Med Chem 52(17):5295–5298Google Scholar
  117. 117.
    Blundell TL, Jhoti H, Abell C (2002) High-throughput crystallography for lead discovery in drug design. Nat Rev Drug Discov 1(1):45–54Google Scholar
  118. 118.
    Hann MM, Leach AR, Harper G (2001) Molecular complexity and its impact on the probability of finding leads for drug discovery. J Chem Inf Comput Sci 41(3):856–864Google Scholar
  119. 119.
    Hartshorn MJ, Murray CW, Cleasby A, Frederickson M, Tickle IJ, Jhoti H (2005) Fragment-based lead discovery using X-ray crystallography. J Med Chem 48(2):403–413Google Scholar
  120. 120.
    Shuker SB, Hajduk PJ, Meadows RP, Fesik SW (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274(5292):1531–1534Google Scholar
  121. 121.
    Wada CK, Holms JH, Curtin ML, Dai Y, Florjancic AS, Garland RB et al (2002) Phenoxyphenyl sulfone N-formylhydroxylamines (retrohydroxamates) as potent, selective, orally bioavailable matrix metalloproteinase inhibitors. J Med Chem 45(1):219–232Google Scholar
  122. 122.
    Howard S, Berdini V, Boulstridge JA, Carr MG, Cross DM, Curry J et al (2009) Fragment-based discovery of the pyrazol-4-yl urea (AT9283), a multitargeted kinase inhibitor with potent aurora kinase activity. J Med Chem 52(2):379–388Google Scholar
  123. 123.
    Wyatt PG, Woodhead AJ, Berdini V, Boulstridge JA, Carr MG, Cross DM et al (2008) Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H-pyrazole-3-carboxamide (AT7519), a novel cyclin dependent kinase inhibitor using fragment-based X-ray crystallography and structure based drug design. J Med Chem 51(16):4986–4999Google Scholar
  124. 124.
    Artis DR, Lin JJ, Zhang C, Wang W, Mehra U, Perreault M et al (2009) Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent. Proc Natl Acad Sci USA 106(1):262–267Google Scholar
  125. 125.
    de Kloe GE, Bailey D, Leurs R, de Esch IJ (2009) Transforming fragments into candidates: small becomes big in medicinal chemistry. Drug Discov Today 14(13–14):630–646Google Scholar
  126. 126.
    Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D (2006) Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc Natl Acad Sci USA 103(21):8060–8065Google Scholar
  127. 127.
    Brooun A, Foster SA, Chrencik JE, Chien EY, Kolatkar AR, Streiff M et al (2007) Remedial strategies in structural proteomics: expression, purification, and crystallization of the Vav1/Rac1 complex. Protein Expr Purif 53(1):51–62Google Scholar
  128. 128.
    Mukherjee S, Zhang Y (2011) Protein-protein complex structure predictions by multimeric threading and template recombination. Structure 19(7):955–966Google Scholar
  129. 129.
    Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450(7172):1001–1009Google Scholar
  130. 130.
    Rosenbaum DM, Cherezov V, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS et al (2007) GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function. Science 318(5854):1266–1273Google Scholar
  131. 131.
    Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS et al (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318(5854):1258–1265Google Scholar
  132. 132.
    Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY, Lane JR et al (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322(5905):1211–1217Google Scholar
  133. 133.
    Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V et al (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330(6007):1066–1071Google Scholar
  134. 134.
    Chien EY, Liu W, Zhao Q, Katritch V, Han GW, Hanson MA et al (2010) Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science 330(6007):1091–1095Google Scholar
  135. 135.
    Chaudhuri TK, Paul S (2006) Protein-misfolding diseases and chaperone-based therapeutic approaches. FEBS J 273(7):1331–1349Google Scholar
  136. 136.
    Pey AL, Ying M, Cremades N, Velazquez-Campoy A, Scherer T, Thony B et al (2008) Identification of pharmacological chaperones as potential therapeutic agents to treat phenylketonuria. J Clin Invest 118(8):2858–2867Google Scholar
  137. 137.
    Bateman KS, Cherney MM, Mahuran DJ, Tropak M, James MN (2011) Crystal structure of beta-hexosaminidase B in complex with pyrimethamine, a potential pharmacological chaperone. J Med Chem 54(5):1421–1429Google Scholar
  138. 138.
    Lieberman RL, Wustman BA, Huertas P, Powe AC Jr, Pine CW, Khanna R et al (2007) Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease. Nat Chem Biol 3(2):101–107Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Wyatt W. Yue
    • 1
  • D. Sean Froese
    • 1
  • Paul E. Brennan
    • 1
  1. 1.Structural Genomics ConsortiumUniversity of OxfordOxfordUK

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