Journal of Computer-Aided Molecular Design

, Volume 8, Issue 6, pp 709–730 | Cite as

Pharmacophore refinement of gpIIb/IIIa antagonists based on comparative studies of antiadhesive cyclic and acyclic RGD peptides

  • Gerhard Müller
  • Marion Gurrath
  • Horst Kessler
Research Papers


Structurally guided design approaches to low-molecular-weight platelet aggregation antagonists addressing the platelet-associated heterodimeric cell surface receptor gpIIb/IIIa rely on comparative studies of an ensemble of conformationally and biologically characterized compounds, since no high-resolution structure of the receptor system is available. We report a classical indirect and comparative pharmacophore refinement approach based on a series of small cyclic Arg-Gly-Asp (RGD) peptides as gpIIb/IIIa-fibrinogen interaction antagonists. These peptides have previously been investigated as potent and selective tumor cell adhesion inhibitors. The definition of geometrical descriptors classifying the RGD peptide conformations and their subsequent analysis over selected RGD- and RXD-containing protein structures allows for a correlation of distinct structural features for platelet aggregation inhibition. An almost parallel alignment of the Arg and Asp side chains was identified by a vector analysis as being present in all active cyclic hexa-and pentapeptides. This orientation is induced mainly by the constraint of backbone cyclization and is not of any covalent tripeptide-inherent origin, which was rationalized by a 500 ps high-energy MD simulation of a sequentially related linear model peptide. The incorporation of the recognition tripeptide Arg-Gly-Asp into the cyclic peptide templates acted as a filter mechanism, restricting the otherwise free torsional relation of both side chains to a parallel orientation. Based on the derived results, several detailed features of the receptor binding site could be deduced in terms of receptor complementarity. These findings should govern the design of next-generation compounds with enhanced activities. Furthermore, the complementary stereochemical characteristics of the substrate can be used as boundary conditions for pseudoreceptor modelling studies that are capable of reconstructing a hypothetical binding pocket, qualitatively resembling the steric and electronic demands of gpIIb/IIIa. It is interesting to note that these features provide clear differentiation to requirements for inhibition of % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9qq-f0-yqaqVeLsFr0-vr% 0-vr0db8meaabaqaciGacaGaaeqabaWaaeaaeaaakeaacaqGXoWaaS% baaSqaaiaabAfadaWgaaadbaaabeaaaSqabaGccaqGYoWaaSbaaSqa% aiaaiodaaeqaaaaa!3DDC!\[{\text{\alpha }}_{{\text{V}}_{} } {\text{\beta }}_3 \] substrate binding. This can account for the extremely high selectivity and activity of some of our constrained peptides for either the % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9qq-f0-yqaqVeLsFr0-vr% 0-vr0db8meaabaqaciGacaGaaeqabaWaaeaaeaaakeaacaqGXoWaaS% baaSqaaiaab+bbcaqGIbaabeaakiaabk7adaWgaaWcbaGaaG4maaqa% baaaaa!3E56!\[{\text{\alpha }}_{{\text{b}}} {\text{\beta }}_3 \] or the % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9qq-f0-yqaqVeLsFr0-vr% 0-vr0db8meaabaqaciGacaGaaeqabaWaaeaaeaaakeaacaqGXoWaaS% baaSqaaiaabAfaaeqaaOGaaeOSdmaaBaaaleaacaaIZaaabeaaaaa!3DA4!\[{\text{\alpha }}_{\text{V}} {\text{\beta }}_3 \] receptor.

Key words

Arg-Gly-Asp peptides Adhesion antagonista Peptide templates Conformational restriction Vector analysis Structure-activity relationships 


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  1. 1.
    ClaasenV. (Ed.) Trends in Drug Research, Elsevier Amsterdam, 1990.Google Scholar
  2. 2.
    MarshallG.R., In BeddellC.R. (Ed.) The Design of Drugs to Macromolecular Targets, Wiley, New York, NY, 1992, pp. 1–24.Google Scholar
  3. 3.
    RosenM.K. and SchreiberS.L., Angew. Chem., Int. Ed. Engl., 31 (1993) 384.Google Scholar
  4. 4.
    VanDuyneG.D., StandaertR.F., KarplusP.A., SchreiberS.L. and ClardyJ., Science, 252 (1991) 839.Google Scholar
  5. 5.
    VanDuyneG.D., StandaertR.F., SchreiberS.L. and ClardyJ., J. Am. Chem. Soc., 113 (1991) 7433.Google Scholar
  6. 6.
    WeberC., WiderG., VonFreybergB., TraberR., BraunW., WidmerH. and WüthrichK., Biochemistry, 30 (1991) 6563.Google Scholar
  7. 7.
    FesikS.W., ClampeJr.R.T., EatonH.L., GemmeckerG., OlejniczakE.T., NeriR., HolzmanT.F., EganD.A., EdaljiR., SimmerB., HelfrichR., HochlowskiJ. and JacksonM., Biochemistry, 30 (1991) 6374.Google Scholar
  8. 8.
    RichardsW.G. (Ed.) Computer-Aided Molecular Design Oxford University Press, London, 1989.Google Scholar
  9. 9.
    PerunT.J. and PropstC.L. (Eds.) Computer-Aided Drug Design, Methods and Applications, Mareel Dekker, New York, NY, 1989.Google Scholar
  10. 10.
    KuntzI.D., Science, 357 (1992) 1078.Google Scholar
  11. 11.
    KessierH., HauptA. and WillM. In PerunT.J. and PropstC.L. (Eds.) Computer-Aided Drug Design, Methods and Applications, Marcel Dekker, New York, NY, 1989, pp. 461–483.Google Scholar
  12. 12.
    KesslerH., Angew. Chem., Int. Ed. Engl., 21 (1982) 512.Google Scholar
  13. 13.
    HrubyV., Life Sci., 31 (1983) 189.Google Scholar
  14. 14.
    GurrathM., MüllerG., KesslerH., AumailleyM. and TimplR., Eur. J. Biochem., 210 (1992) 911.Google Scholar
  15. 15.
    GartnerT.K. and BennettJ.S., J. Biol. Chem., 260 (1985) 11891.Google Scholar
  16. 16.
    KloozewiakM., TimmonsS., LukasT.J. and HawigarJ., Biochemistry, 23 (1984) 1767.Google Scholar
  17. 17.
    LamS.C.-T., PlowE.F., SmithM.A., AndrieuxA., RyckwaertJ.-J., MarguerieG. and GinsbergM.H., J. Biol. Chem., 262 (1987) 947.Google Scholar
  18. 18.
    NicholsA.J., RuffoloJr.R.R., HuffmanW.F., PosteG. and SamanenJ., Trends Pharmacol. Sci., 13 (1992) 413.Google Scholar
  19. 19.
    RuoslahtiE. and PierschbacherM.D., Science, 238 (1987) 491.Google Scholar
  20. 20.
    HynesR.O., Cell, 48 (1987) 549.Google Scholar
  21. 21.
    AlbedaS.M. and BuekC.A., FASEB J., 4 (1990) 2868.Google Scholar
  22. 22.
    HumphriesM.J., J. Cell Sci., 97 (1990) 585.Google Scholar
  23. 23.
    DamskyC.H. and BernfieldM., Curr. Opin. Cell Biol., 2 (1990) 813.Google Scholar
  24. 24.
    D'SouzaS.E., GinsbergM.H. and PlowE.F., Trends Biochem. Sci., 16 (1991) 246.Google Scholar
  25. 25.
    PierschbacherM.D. and RuoslahtiE., Nature, 309 (1984) 30.Google Scholar
  26. 26.
    PierschbacherM.D. and RuoslahtiE., Proc. Natl. Acad. Sci. USA, 81 (1984) 5985.Google Scholar
  27. 27.
    YamadaK.M., J. Biol. Chem., 266 (1991) 12809.Google Scholar
  28. 28.
    PierschbacherM.D. and RuoslahtiE., J. Biol. Chem., 262 (1987) 17924.Google Scholar
  29. 29.
    GehlsenK.R., ArgravesW.S., PierschbacherM.D. and RuoslahtiE., J. Cell Biol., 106 (1984) 925.Google Scholar
  30. 30.
    HautanenA., GailitJ., MannD.M. and RuoslahtiE., J. Biol. Chem., 264 (1989) 1437.Google Scholar
  31. 31.
    SamanenJ., AliF.E., RomoffT., CalvoR., SørensenE., BennettD., BerryD., KosterP., VaskoJ., PowersD., StadelJ. and NicholsA., In GiraltE. and AndreuD. (Eds.) Peptides 1990 (Proceedings of the 21st European Peptide Symposium), ESCOM, Leiden, 1991, pp. 781–783.Google Scholar
  32. 32.
    NuttR.F., BradyS.F., SiskoJ.T., CiccaroneT.M., ColtonC.D., LevyM.R., GouldR.J., ZhangG., FriedmanP.A. and VeberD.F., In GiraltE. and AndreuD. (Eds.) Peptides 1990 (Proceedings of the 21st European Peptide Symposium), ESCOM, Leiden, 1991, pp. 784–786.Google Scholar
  33. 33.
    SamanenJ., AliF., RomoffT., CalvoR., SørensenE., VaskoJ., StorerB., BerryD., BennettD., StrohsackerM., PowersD., StadelJ. and NicholsA., J. Med. Chem., 34 (1991) 3114.Google Scholar
  34. 34.
    AumailleyM., GurrathM., MüllerG., CalveteJ., TimplR. and KesslerH., FEBS Lett., 291 (1991) 50.Google Scholar
  35. 35.
    ScarboroughR.M., NaughtonM.A., TengW., RoseJ.W., PhillipsD.R., NannizziL., ArfstenA., CampbellA.M. and CharoI.F., J. Biol. Chem., 268 (1993) 1066.Google Scholar
  36. 36.
    ChengS., CraigW.S., MullenD., TschoppJ.F., DixonD. and PierschbacherM.D., J. Med. Chem., 37 (1994) 1.Google Scholar
  37. 37.
    KleinS.I., MolinoB.F., ChuV., RuggeriZ., CzekajM., GardnerC.J., NewmanJ. and BarrettJ.A., In GiraltE. and AndreuD. (Eds.) Peptides 1990 (Proceedings of the 21st European Peptide Symposium), ESCOM, Leiden, 1991, pp. 374–375.Google Scholar
  38. 38.
    CallahanJ.F., BeanJ.W., BurgessJ.L., EgglestonD.S., HwangS.M., KoppleK.D., KosterP.F., NicholsA., PeishoffC.E., SamanenJ.M., VaskoJ.A., WongA. and HuffmanW.F., J. Med. Chem., 35 (1992) 3970.Google Scholar
  39. 39.
    AligL., EdenhoferA., HadváryP., HürzelerM., KnoppD., MüllerM., SteinerB., TrzeciakA. and WellerT., J. Med. Chem., 35 (1992) 4393.Google Scholar
  40. 40.
    GreenspoonN., HershkovizR., AlonR., VaronD., ShenkmanB., MarxG., FedermanS., KapustinaG. and LiderO., Biochemistry, 32 (1993) 1001.Google Scholar
  41. 41.
    GanZ.-R., GouldR.J., JacobsJ.W., FriedmanP.A. and PolokoffM.A., J. Biol. Chem., 263 (1988) 19827.Google Scholar
  42. 42.
    DennisM.S., HenzelW.J., PittiR.M., LipariM.T., NapierM.A., DeisherT.A., BuntingS. and LazarusR.A., Proc. Natl. Acad. Sci. USA, 87 (1989) 2471.Google Scholar
  43. 43.
    WilliamsJ., RucinskiB., HoltJ. and NiewiarowskiS., Biochim. Biophys. Acta, 1039 (1990) 81.Google Scholar
  44. 44.
    SoszkaT., KnudsenK.A., BevigliaL., RossiC., PoggiA. and NiewiarowskiS., Exp. Cell Res., 196 (1991) 6.Google Scholar
  45. 45.
    ShebuskiR.J., RamjitD.R., BencenG.H. and PolokoffM.A., J. Biol. Chem., 264 (1989) 21550.Google Scholar
  46. 46.
    HuangT.-F., HoltJ.C., KirbyE.P. and NiewiarowskiS., Biochemistry, 28 (1989) 661.Google Scholar
  47. 47.
    SavageB., MarzecU.M., ChaoB.H., HarkerL.A., MaraganoreJ.M. and RuggeriZ.M., J. Biol. Chem., 265 (1990) 11766.Google Scholar
  48. 48.
    SatoM., SardanaM.K., GrasserW.A., GarkyV.M., MurrayJ.M. and GouldR.J., J. Cell Biol., 111 (1990) 1713.Google Scholar
  49. 49.
    PfaffM., TangemannK., MüllerB., GurrathM., MüllerG., KesslerH., TimplR. and EngelJ., J. Biol. Chem., 269 (1994) 20233.Google Scholar
  50. 50.
    BartlettR.A., SheaG.T., TelferS.J. and WatermanS., In RobertsS.M. (Ed.) Molecular Recognition: Chemical and Biochemical Problems, The Royal Society of Chemistry, Cambridge, 1989, pp. 182–196.Google Scholar
  51. 51.
    AdlerM., LazarusR.A., DennisM.S. and WagnerG., Science, 253 (1991) 445.Google Scholar
  52. 52.
    SaudekV., AtkinsonP.A. and PeltonJ., Biochemistry 30 (1991) 7369.Google Scholar
  53. 53.
    DalvitC., WidmerH., BovermannG., BrockenridgeR. and MetternichR., Eur. J. Biochem., 202 (1991) 315.Google Scholar
  54. 54.
    CookeR.M., CarterB.G., MartinD.M.A., Murray-RustP. and WeirM.P., Eur. J. Biochem., 202 (1991) 323.Google Scholar
  55. 55.
    Dauber-OsguthorpeP., RobertsV.A., OsguthorpeD.J., WolffJ., GenestM. and HaglerA.T., Protein Struct. Funct. Genet., 4 (1988) 31.Google Scholar
  56. 56.
    VeristL., Phys. Rev., 159 (1967) 98.Google Scholar
  57. 57.
    PfaffM., AumailleyM., SpecksU., KnolleJ., ZerwesH.G. and TimplR., Exp. Cell Res., 206 (1993) 167.Google Scholar
  58. 58.
    MüllerG., GurrathM., KesslerH. and TimplR., Angew. Chem., Int. Ed. Engl., 31 (1992) 326.Google Scholar
  59. 59.
    MüllerG., GurrathM., KurzM. and KesslerH., Protein Struct. Funct. Genet., 15 (1993) 235.Google Scholar
  60. 60.
    WistowG., TurnellB., SummersL., SlingsbyC., MossD., MillerL., LindleyP. and BlundellT., J. Mol. Biol., 107 (1983) 175.Google Scholar
  61. 61.
    KurzM., MierkeD.F. and KesslerH., Angew. Chem., Int. Ed. Engl., 31 (1992) 210.Google Scholar
  62. 62.
    BoguskyM.J., NaylorA.M., PitzenbergerS.M., NuttR.F., BradyS.F., ColtonC.D., SiskoJ.T., AndersonP.S. and VeberD.F., Int. J. Pept. Protein Res. 39 (1992) 63.Google Scholar
  63. 63.
    PeishoffC.E., AliF.E., BeanJ.W., CalveR., D'AmbrosioA.D., EgglestonD.S., HwangS.M., KlineT.P., KosterP.F., NicholsA., PowersD., RomoffT., SamanenJ.M., StadelJ., VaskoJ.A. and KoppleK.D., J. Med. Chem. 35 (1992) 3962.Google Scholar
  64. 64.
    CotraitM., KreisslerM., HoflackJ., LehnJ.-M. and MaigretB., J. Comput.-Aided Mol. Design, 6 (1992) 113.Google Scholar
  65. 65.
    SiahaanT., LarkL.R., PierschbacherM.D., RuoslahtiE. and GieraschL.M., In RivierJ.E. and MarshallG.R., (Eds.) Peptides: Chemistry, Structure and Biology (Proceedings of the 11th American Peptide Symposium), ESCOM, Leiden, 1990, pp. 699–701.Google Scholar
  66. 66.
    RuoslahtiE. and PlerschbacherM.D., Science, 238 (1987) 491.Google Scholar
  67. 67.
    BeanJ.W., KoppleK.D. and PeishoffC.E., J. Am. Chem. Soc., 114 (1992) 5328.Google Scholar
  68. 68.
    KoppleK.D., BauresP.W., BeanJ.W., D'AmbrosioC.A., HughesJ.L., PeishoffC.E. and EgglestonD.S., J. Am. Chem. Soc., 114 (1992) 9615.Google Scholar
  69. 69.
    Gurrath, M., Ph.D. Thesis, Technischo Universität München, Garching, 1992.Google Scholar
  70. 70.
    Müller, G., Ph.D. Thesis, Technischo Universität München, Garching, 1992.Google Scholar
  71. 71.
    LenderA., YaoW., SprengelerP.A., SpanevelloR.A., FurstG.T., HirschmannR. and SmithIIIA.B., Int. J. Pept. Protein Res., 42 (1993) 509.Google Scholar
  72. 72.
    JohnsonJr.W.C., PaganoT.G., BassonC.T., MadriJ.A., GooleyP. and ArmitageI.M., Biochemistry, 32 (1993) 268.Google Scholar
  73. 73.
    BarkerP.L., BullensS., BuntingS., BurdiekD.J., ChanK.S., DeisherT., EigenbrotC., GadekT.R., GantzosR., LipariM.T., MuirC.D., NapierM.A., PittiR.M., PaduaA., QuanC., StanleyM., StrubleM., TomJ.Y.K. and BrunierJ.P., J. Med. Chem., 35 (1992) 2040.Google Scholar
  74. 74.
    O'NeilK.T., HoessR.H., JacksonS.A., RamachandranN.S., MousaS.A. and DeGradoW.F., Protein Struct. Funct. Genet., 14 (1992) 509.Google Scholar
  75. 75.
    LamK.S., SalmonS.E., HerschE.M., HrubyV.J., KazmierskiW.M. and KnappR.J., Nature, 354 (1991) 82.Google Scholar
  76. 76.
    HoughtenR.A., PinillaC., BlondelleS.E., AppleJ.R., DooleyC.T. and CuervoJ.H., Nature, 354 (1991) 84.Google Scholar
  77. 77.
    ScottJ.K. and SmithG.P., Science, 249 (1990) 386.Google Scholar
  78. 78.
    DelvinJ.J., PanganibanL.C. and DevlinP.E., Science, 249 (1990) 404.Google Scholar
  79. 79.
    CwirlaS.E., PetersE.A., BarrettR.W. and DowerW.J., Proc. Natl. Acad. Sci. USA, 87 (1990) 6378.Google Scholar
  80. 80.
    FeliciF., CastagnoliL., MusacchioA., JappelliR. and CesareniG., J. Mol. Biol., 222 (1991) 301.Google Scholar
  81. 81.
    JungG. and Beck-SickingerA.G., Angew. Chem., Int. Ed. Engl., 31 (1992) 367.Google Scholar
  82. 82.
    SimonR.J., KaniaR.S., ZuckermannR.N., HuebnerV.D., JewellD.A., BanvilleS., NgS., WangL., RosenbergS., MarloweC.K., SpellmeyerD.C., TanR., FrankelA.D., SantiD.V., CohenF.E. and BarlettP.A., Proc. Natl. Acad. Sci. USA, 89 (1992) 9367.Google Scholar
  83. 83.
    KesslerH., Angew. Chem., Int. Ed. Engl., 32 (1993) 543.Google Scholar
  84. 84.
    HolmesM.A., TronrudD.E. and MatthewsB.W., Biochemistry, 22 (1983) 236.Google Scholar
  85. 85.
    CarterD.C., MelisK.A., O'DonnellS.E., BurgessB.K., FureyJr.W.F., WangB.-C. and ScottC.D., J. Mol. Biol., 184 (1985) 279.Google Scholar
  86. 86.
    RyuS.-E., KwongP.D., TrunehA., PorterT.G., ArthosJ., RosenbergM., DaiX., XuongN.-H., AxelR., SweetR.W. and HendricksonW.A., Nature 348 (1990) 419.Google Scholar
  87. 87.
    FujinagaM., DelbaereL.T.J., BrayerG.D. and JamesM.N.G., J. Mol. Biol., 184 (1985) 479.Google Scholar
  88. 88.
    OchiH., HataY., TanakaN., KakudoM., SakuraiT., AiharaS. and MoritaY., J. Mol. Biol., 166 (1983) 407.Google Scholar
  89. 89.
    LeshyD.J., HendricksonW.A., AukhilI. and EricksonH.P., Science, 258 (1992) 987.Google Scholar

Copyright information

© ESCOM Science Publishers B.V 1994

Authors and Affiliations

  • Gerhard Müller
    • 1
  • Marion Gurrath
    • 1
  • Horst Kessler
    • 1
  1. 1.Institut für Organische Chemie und BiochemicTechnische Universität MünchenGarchingGermany

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