Journal of Computer-Aided Molecular Design

, Volume 20, Issue 3, pp 159–178 | Cite as

Discovering New Classes of Brugia malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change

  • Sai Chetan K. Sukuru
  • Thibaut Crepin
  • Youli Milev
  • Liesl C. Marsh
  • Jonathan B. Hill
  • Regan J. Anderson
  • Jonathan C. Morris
  • Anjali Rohatgi
  • Gavin O’Mahony
  • Morten Grøtli
  • Franck Danel
  • Malcolm G. P. Page
  • Michael Härtlein
  • Stephen Cusack
  • Michael A. Kron
  • Leslie A. Kuhn
Original Paper


SLIDE software, which models the flexibility of protein and ligand side chains while docking, was used to screen several large databases to identify inhibitors of Brugia malayi asparaginyl-tRNA synthetase (AsnRS), a target for anti-parasitic drug design. Seven classes of compounds identified by SLIDE were confirmed as micromolar inhibitors of the enzyme. Analogs of one of these classes of inhibitors, the long side-chain variolins, cannot bind to the adenosyl pocket of the closed conformation of AsnRS due to steric clashes, though the short side-chain variolins identified by SLIDE␣apparently bind isosterically with adenosine. We hypothesized that an open conformation of the motif 2 loop also permits the long side-chain variolins to bind in the adenosine pocket and that their selectivity for Brugia relative to human AsnRS can be explained by differences in the sequence and conformation of this loop. Loop flexibility sampling using Rigidity Optimized Conformational Kinetics (ROCK) confirms this possibility, while scoring of the relative affinities of the different ligands by SLIDE correlates well with the compounds’ ranks in inhibition assays. Combining ROCK and SLIDE provides a promising approach for exploiting conformational flexibility in structure-based screening and design of species selective inhibitors.

Key words

Conformational flexibility Docking Inhibitor design Sampling Scoring Screening Anti-parasitic agents MSU ProFlex ROCK SLIDE 



aminoacyl-tRNA synthetases


asparaginyl sulfamoyl adenylate


asparaginyl-tRNA synthetase


Cambridge Structural Database


l-aspartate-β-hydroxamate adenylate


molecular dynamics


Protein Data Bank


S-methyl-deoxyvariolin B


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.



We thank Dr. Paul Sanschagrin for his initial CSD screening that identified variolin B as an inhibitor, and Dr. Maria Zavodszky for her assistance with ROCK. We also thank NCI for providing us with samples of plated compounds and Dr. Samuel Danishefsky for providing us with rishirilide B. Drs. Holger Gohlke and Gerhard Klebe, Dr. Shaomeng Wang, and OpenEye Scientific Software (Santa Fe, NM) generously provided their DrugScore, X-Score, and Omega software for our use. This work was supported by NIH grants GM 67249 to L.A.K. and U01 AI53877 to M.A.K., S.C., M.G.P.P., F.D., and L.A.K.


  1. 1.
    Lazdins J, Kron M (1999) Parasitol Today 15:305CrossRefGoogle Scholar
  2. 2.
    Melrose WD (2002) Int J Parasitol 32:947CrossRefGoogle Scholar
  3. 3.
    Kron MA, Kuhn LA, Sanschagrin PC, Härtlein M, Grøtli M, Cusack S (2003) J Parasitol 89(Suppl):S226Google Scholar
  4. 4.
    Brown KR, Ricci FM, Ottesen EA (2000) Parasitology 121:S133CrossRefGoogle Scholar
  5. 5.
    Horton J, Witt C, Ottesen EA, Lazdins JK, Addiss DG, Awadzi K, Beach MJ, Belizario VY, Dunyo SK, Espinel M, Gyapong JO, Hossain M, Ismail MM, Jayakody RL, Lammie PJ, Makunde W, Richard-Lenoble D, Selve B, Shenoy RK, Simonsen PE, Wamae CN, Weerasooriya MV (2000) Parasitology 121:S147CrossRefGoogle Scholar
  6. 6.
    Schimmel P, Tao JS, Hill J (1998) FASEB J 12:1599Google Scholar
  7. 7.
    Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990) Nature 347:203CrossRefGoogle Scholar
  8. 8.
    Cusack S, Berthet-Colominas C, Härtlein M, Nassar N, Leberman R (1990) Nature 347:249CrossRefGoogle Scholar
  9. 9.
    Woese CR, Olsen GJ, Ibba M, Soll D (2000) Microbiol Mol Biol Rev 64:202CrossRefGoogle Scholar
  10. 10.
    Brown MJB, Mensah LM, Doyle ML, Broom NJP, Osbourne N, Forrest AK, Richardson CM, Oȁ9Hanlon PJ, Pope AJ (2000) Biochemistry 39:6003CrossRefGoogle Scholar
  11. 11.
    Casewell MW, Hill RLR (1985) J Antimicrob Chemoth 15:523CrossRefGoogle Scholar
  12. 12.
    Hughes J, Mellows G (1980) Biochem J 191:209Google Scholar
  13. 13.
    Nilsen TW, Maroney PA, Goodwin RG, Perrine KG, Denker JA, Nanduri J, Kazura JW (1988) Proc Natl Acad Sci USA 85:3604CrossRefGoogle Scholar
  14. 14.
    Kron M, Petridis M, Milev Y, Leykam J, Härtlein M (2003) Mol Biochem Parasitol 129:33CrossRefGoogle Scholar
  15. 15.
    Ramirez BL, Howard OMZ, Dock HF, Edamatsu T, Gao P, Härtlein M, Kron M (2006 in press) J Infect DisGoogle Scholar
  16. 16.
    Kron M, Marquard K, Härtlein M, Price S, Leberman R (1995) FEBS Lett 7374:122CrossRefGoogle Scholar
  17. 17.
    Beaulande M, Tarbouriech N, Härtlein M (1998) Nucleic Acids Res 26:521CrossRefGoogle Scholar
  18. 18.
    Doucet JP, Weber J (1996) Molecular similarity, in Computer-Aided Molecular Design: Theory and Applications. Academic Press, San Diego, CA p 328Google Scholar
  19. 19.
    Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK (2002) J Med Chem 45:2213CrossRefGoogle Scholar
  20. 20.
    Schnecke V, Swanson CA, Getzoff ED, Tainer JA, Kuhn LA (1998) Proteins 33:74CrossRefGoogle Scholar
  21. 21.
    Carlson HA, McCammon JA (2000) Mol Pharmacol 57:213Google Scholar
  22. 22.
    Knegtel RMA, Kuntz ID, Oshiro CM (1997) J Mol Biol 266:424CrossRefGoogle Scholar
  23. 23.
    Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS (2002) Proteins 46:34CrossRefGoogle Scholar
  24. 24.
    Claussen H, Buning C, Rarey M, Lengauer T (2001) J Mol Biol 308:377CrossRefGoogle Scholar
  25. 25.
    Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA (2000) J Med Chem 43:2100CrossRefGoogle Scholar
  26. 26.
    Schnecke V, Kuhn LA (1999) Proc Int Conf Intell Syst Mol Biol 242Google Scholar
  27. 27.
    Zavodszky MI, Sanschagrin PC, Korde RS, Kuhn LA (2002) J Comput Aid Mol Des 16:883CrossRefGoogle Scholar
  28. 28.
    Zavodszky MI, Kuhn LA (2006 in review) ProteinsGoogle Scholar
  29. 29.
    Zavodszky MI, Kuhn LA (2005) Protein Sci 14:1104CrossRefGoogle Scholar
  30. 30.
    Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Proteins 44:150CrossRefGoogle Scholar
  31. 31.
    Lei M, Zavodszky MI, Kuhn LA, Thorpe MF (2004) J Comput Chem 25:1133CrossRefGoogle Scholar
  32. 32.
    Zavodszky MI, Lei M, Thorpe MF, Day AR, Kuhn LA (2004) Proteins 57:243CrossRefGoogle Scholar
  33. 33.
    Berthet-Colominas C, Crepin T, Haertlein M, Kron M, Cusack S (in preparation)Google Scholar
  34. 34.
    Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Acta Crystallogr D 54:905CrossRefGoogle Scholar
  35. 35.
    Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283CrossRefGoogle Scholar
  36. 36.
    Hess HH, Derr JE (1975) Anal Biochem 63:607CrossRefGoogle Scholar
  37. 37.
    Baykov AA, Evtushenko OA, Avaeva SM (1988) Anal Biochem 171:266CrossRefGoogle Scholar
  38. 38.
    Cogan EB, Birrell GB, Griffith OH (1999) Anal Biochem 271:29CrossRefGoogle Scholar
  39. 39.
    Danel F, Walle C, Kron M, Haertlein M, Cusack S, Page MGP (2004) International Conference on Aminoacyl tRNA Synthetases. Seoul National University, Seoul, Korea, p 115Google Scholar
  40. 40.
    Schnecke V, Kuhn LA (2000) Perspect Drug Discov 20:171CrossRefGoogle Scholar
  41. 41.
    Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL (2004) J Med Chem 47:3032CrossRefGoogle Scholar
  42. 42.
    Perola E, Walters WP, Charifson PS (2004) Proteins 56:235CrossRefGoogle Scholar
  43. 43.
    Halperin I, Ma BY, Wolfson H, Nussinov R (2002) Proteins 47:409CrossRefGoogle Scholar
  44. 44.
    Stahl M, Rarey M (2001) J Med Chem 44:1035CrossRefGoogle Scholar
  45. 45.
    Bissantz C, Folkers G, Rognan D (2000) J Med Chem 43:4759CrossRefGoogle Scholar
  46. 46.
    Gohlke H, Hendlich M, Klebe G (2000) J Mol Biol 295:337CrossRefGoogle Scholar
  47. 47.
    Wang RX, Lai LH, Wang SM (2002) J Comput Aid Mol Des 16:11CrossRefGoogle Scholar
  48. 48.
    Hespenheide BM, Rader AJ, Thorpe MF, Kuhn LA (2002) J Mol Graph Model 21:195CrossRefGoogle Scholar
  49. 49.
    Rader AJ, Hespenheide BM, Kuhn LA, Thorpe MF (2002) Proc Natl Acad Sci USA 99:3540CrossRefGoogle Scholar
  50. 50.
    Taylor R (2002) Acta Crystallogr D 58:879CrossRefGoogle Scholar
  51. 51.
    Ihlenfeldt WD, Voigt JH, Bienfait B, Oellien F, Nicklaus MC (2002) J Chem Inf Comp Sci 42:46CrossRefGoogle Scholar
  52. 52.
    Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Adv Drug Deliver Rev 46:3CrossRefGoogle Scholar
  53. 53.
    Perry NB, Ettouati L, Litaudon M, Blunt JW, Munro MHG, Parkin S, Hope H (1994) Tetrahedron 50:3987CrossRefGoogle Scholar
  54. 54.
    Evers DL, Breitenbach JM, Borysko KZ, Townsend LB, Drach JC (2002) Antimicrob Agents Ch 46:2470CrossRefGoogle Scholar
  55. 55.
    Gompel M, Leost M, Joffe EBD, Puricelli L, Franco LH, Palermo J, Meijer L (2004) Bioorg Med Chem Lett 14:1703CrossRefGoogle Scholar
  56. 56.
    Anderson RJ, Morris JC (2001) Tetrahedron Lett 42:8697CrossRefGoogle Scholar
  57. 57.
    Anderson RJ, Morris JC (2001) Tetrahedron Lett 42:311CrossRefGoogle Scholar
  58. 58.
    Anderson RJ, Hill JB, Morris JC (2005) J Org Chem 70:6204CrossRefGoogle Scholar
  59. 59.
    Anderson RJ (2002) Total synthesis of variolin B. PhD Thesis, Department of Chemistry, University of Canterbury, Christchurch, NZGoogle Scholar
  60. 60.
    Marsh LC (2005) Synthetic studies on marine natural products. MSc Thesis, Department of Chemistry, University of Canterbury, Christchurch, NZGoogle Scholar
  61. 61.
    Hill JB (2005) Deoxyvariolins and polymer therapeutics. PhD Thesis, Department of Chemistry, University of Canterbury, Christchurch, NZGoogle Scholar
  62. 62.
    Saffer JD, Glazer RI (1981) Mol Pharmacol 20:211Google Scholar
  63. 63.
    Davies LP, Jamieson DD, Baird-Lambert JA, Kazlauskas R (1984) Biochem Pharmacol 33:347CrossRefGoogle Scholar
  64. 64.
    Recchia I, Rucci N, Festuccia C, Bologna M, MacKay AR, Migliaccio S, Longo M, Susa M, Fabbro D, Teti A (2003) Eur J Cancer 39:1927CrossRefGoogle Scholar
  65. 65.
    Recchia I, Rucci N, Funari A, Migliaccio S, Taranta A, Longo M, Kneissel M, Susa M, Fabbro D, Teti A (2004) Bone 34:65CrossRefGoogle Scholar
  66. 66.
    Sadowski J, Gasteiger J (1993) Chem Rev 93:2567CrossRefGoogle Scholar
  67. 67.
    Allen JG, Danishefsky SJ (2001) J Am Chem Soc 123:351CrossRefGoogle Scholar
  68. 68.
    Neidle S, Taylor GL, Cowling PC (1979) Acta Crystallogr B 35:708CrossRefGoogle Scholar
  69. 69.
    Freist W, Wiedner H, Cramer F (1980) Bioorg Chem 9:491CrossRefGoogle Scholar
  70. 70.
    Dhananjeyan MR, Milev YP, Kron MA, Nair MG (2005) J Med Chem 48:2822CrossRefGoogle Scholar
  71. 71.
    Burnouf C, Pruniaux MP (2002) Curr Pharm Design 8:1255CrossRefGoogle Scholar
  72. 72.
    Klenke B, Barrett MP, Brun R, Gilbert IH (2003) J Antimicrob Chemother 52:290CrossRefGoogle Scholar
  73. 73.
    Goble FC (1950) J Pharmacol Exp Ther 98:49Google Scholar
  74. 74.
    Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D (1991) Science 252:1682CrossRefGoogle Scholar
  75. 75.
    Shiba K, Stello T, Motegi H, Noda T, Musier-Forsyth K, Schimmel P (1997) J Biol Chem 272:22,809CrossRefGoogle Scholar
  76. 76.
    Cusack S, Yaremchuk A, Tukalo M (1996) EMBO J 15:2834Google Scholar
  77. 77.
    Burke B, Yang F, Chen F, Stehlin C, Chan B, Musier-Forsyth K (2000) Biochemistry 39:15,540CrossRefGoogle Scholar
  78. 78.
    Yaremchuk A, Tukalo M, Grøtli M, Cusack S (2001) J Mol Biol 309:989CrossRefGoogle Scholar
  79. 79.
    Lenhard B, Filipic S, Landeka I, Skrtic I, Soll D, Weygand-Durasevic I (1997) J Biol Chem 272:1136CrossRefGoogle Scholar
  80. 80.
    Wang P, Vaidehi N, Tirrell DA, Goddard WA (2002) J Am Chem Soc 124:14,442Google Scholar
  81. 81.
    Cramer RD, Patterson DE, Bunce JD (1988) J Am Chem Soc 110:5959CrossRefGoogle Scholar
  82. 82.
    Kim SY, Lee J (2003) Bioorgan Med Chem 11:5325CrossRefGoogle Scholar
  83. 83.
    Finn J, Mattia K, Morytko M, Ram S, Yang YF, Wu XM, Mak E, Gallant P, Keith D (2003) Bioorg Med Chem Lett 13:2231CrossRefGoogle Scholar
  84. 84.
    Lee J, Kim SE, Lee JY, Kim SY, Kang SU, Seo SH, Chun MW, Kang T, Choi SY, Kim HO (2003) Bioorg Med Chem Lett 13:1087CrossRefGoogle Scholar
  85. 85.
    Jarvest RL, Erskine SG, Forrest AK, Fosberry AP, Hibbs MJ, Jones JJ, Oȁ9Hanlon PJ, Sheppard RJ, Worby A (2005) Bioorg Med Chem Lett 15:2305CrossRefGoogle Scholar
  86. 86.
    Bernier S, Akochy PM, Lapointe J, Chenevert R (2005) Bioorgan Med Chem 13:69CrossRefGoogle Scholar
  87. 87.
    Cavasotto CN, Abagyan RA (2004) J Mol Biol 337:209CrossRefGoogle Scholar
  88. 88.
    Gorfe AA, Caflisch A (2005) Structure 13:1487CrossRefGoogle Scholar
  89. 89.
    Gohlke H, Kuhn LA, Case DA (2004) Proteins 56:322CrossRefGoogle Scholar
  90. 90.
    Bursavich MG, Rich DH (2002) J Med Chem 45:541CrossRefGoogle Scholar
  91. 91.
    Finer-Moore JS, Anderson AC, Oȁ9Neil RH, Costi MP, Ferrari S, Krucinski J, Stroud RM (2005) Acta Crystallogr D 61:1320CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Sai Chetan K. Sukuru
    • 1
    • 2
  • Thibaut Crepin
    • 4
  • Youli Milev
    • 3
  • Liesl C. Marsh
    • 5
  • Jonathan B. Hill
    • 5
  • Regan J. Anderson
    • 5
  • Jonathan C. Morris
    • 6
  • Anjali Rohatgi
    • 1
  • Gavin O’Mahony
    • 7
  • Morten Grøtli
    • 7
  • Franck Danel
    • 8
  • Malcolm G. P. Page
    • 8
  • Michael Härtlein
    • 9
  • Stephen Cusack
    • 4
  • Michael A. Kron
    • 1
  • Leslie A. Kuhn
    • 1
    • 2
  1. 1.Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUSA
  2. 2.Quantitative Biology and Modeling InitiativeMichigan State UniversityEast LansingUSA
  3. 3.Department of Medicine and Institute of International HealthMichigan State UniversityEast LansingUSA
  4. 4.European Molecular Biology LaboratoryGrenobleFrance
  5. 5.Department of ChemistryUniversity of CanterburyChristchurchNew Zealand
  6. 6.School of Chemistry and PhysicsThe University of AdelaideAdelaideAustralia
  7. 7.Department of ChemistryGöteborg UniversityGöteborgSweden
  8. 8.Basilea Pharmaceutica LimitedBaselSwitzerland
  9. 9.Large Scale Structures GroupInstitute Laue-LangevinGrenobleFrance

Personalised recommendations