1k21 › Citations

Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.

Dullweber F, Stubbs MT, Musil D, Stürzebecher J, Klebe G
J Mol Biol 313 593-614 (2001)
Related entries: 1k1i, 1k1j, 1k1l, 1k1m, 1k1n, 1k1o, 1k1p, 1k22

Cited: 67 times
EuropePMC logo PMID: 11676542

Abstract

The binding of a series of low molecular weight ligands towards trypsin and thrombin has been studied by isothermal titration calorimetry and protein crystallography. In a series of congeneric ligands, surprising changes of protonation states occur and are overlaid on the binding process. They result from induced pK(a) shifts depending on the local environment experienced by the ligand and protein functional groups in the complex (induced dielectric fit). They involve additional heat effects that must be corrected before any conclusion on the binding enthalpy (DeltaH) and entropy (DeltaS) can be drawn. After correction, trends in both contributions can be interpreted in structural terms with respect to the hydrogen bond inventory or residual ligand motions. For all inhibitors studied, a strong negative heat capacity change (DeltaC(p)) is detected, thus binding becomes more exothermic and entropically less favourable with increasing temperature. Due to a mutual compensation, Gibbs free energy remains virtually unchanged. The strong negative DeltaC(p) value cannot solely be explained by the removal of hydrophobic surface portions of the protein or ligand from water exposure. Additional contributions must be considered, presumably arising from modulations of the local water structure, changes in vibrational modes or other ordering parameters. For thrombin, smaller negative DeltaC(p) values are observed for ligand binding in the presence of sodium ions compared to the other alkali ions, probably due to stabilising effects on the protein or changes in the bound water structure.

Articles - 1k21 mentioned but not cited (3)

  1. Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Singh N, Warshel A. Proteins 78 1705-1723 (2010)
  2. Effects of Cationic Proteins on Gold Nanoparticle/Aptamer Assays. Pires TA, Narovec CM, Whelan RJ. ACS Omega 2 8222-8226 (2017)
  3. Extrapolative prediction using physically-based QSAR. Cleves AE, Jain AN. J. Comput. Aided Mol. Des. 30 127-152 (2016)


Reviews citing this publication (6)

  1. A medicinal chemist's guide to molecular interactions. Bissantz C, Kuhn B, Stahl M. J. Med. Chem. 53 5061-5084 (2010)
  2. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Mobley DL, Dill KA. Structure 17 489-498 (2009)
  3. Adding calorimetric data to decision making in lead discovery: a hot tip. Ladbury JE, Klebe G, Freire E. Nat Rev Drug Discov 9 23-27 (2010)
  4. C1-inhibitor deficiency and angioedema: molecular mechanisms and clinical progress. Cugno M, Zanichelli A, Foieni F, Caccia S, Cicardi M. Trends Mol Med 15 69-78 (2009)
  5. Drugging challenging targets using fragment-based approaches. Coyne AG, Scott DE, Abell C. Curr Opin Chem Biol 14 299-307 (2010)
  6. Peptidomimetic thrombin inhibitors. Kikelj D. Pathophysiol. Haemost. Thromb. 33 487-491 (2003)

Articles citing this publication (58)

  1. Very fast prediction and rationalization of pKa values for protein-ligand complexes. Bas DC, Rogers DM, Jensen JH. Proteins 73 765-783 (2008)
  2. Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody. Midelfort KS, Hernandez HH, Lippow SM, Tidor B, Drennan CL, Wittrup KD. J. Mol. Biol. 343 685-701 (2004)
  3. Design of novel and selective inhibitors of urokinase-type plasminogen activator with improved pharmacokinetic properties for use as antimetastatic agents. Schweinitz A, Steinmetzer T, Banke IJ, Arlt MJ, Stürzebecher A, Schuster O, Geissler A, Giersiefen H, Zeslawska E, Jacob U, Krüger A, Stürzebecher J. J. Biol. Chem. 279 33613-33622 (2004)
  4. Structural parameterization of the binding enthalpy of small ligands. Luque I, Freire E. Proteins 49 181-190 (2002)
  5. The structure of MBL-associated serine protease-2 reveals that identical substrate specificities of C1s and MASP-2 are realized through different sets of enzyme-substrate interactions. Harmat V, Gál P, Kardos J, Szilágyi K, Ambrus G, Végh B, Náray-Szabó G, Závodszky P. J. Mol. Biol. 342 1533-1546 (2004)
  6. Binding-linked protonation of a DNA minor-groove agent. Nguyen B, Stanek J, Wilson WD. Biophys. J. 90 1319-1328 (2006)
  7. Towards an integrated description of hydrogen bonding and dehydration: decreasing false positives in virtual screening with the HYDE scoring function. Reulecke I, Lange G, Albrecht J, Klein R, Rarey M. ChemMedChem 3 885-897 (2008)
  8. Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments. Czodrowski P, Sotriffer CA, Klebe G. J. Mol. Biol. 367 1347-1356 (2007)
  9. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Proteins 65 424-437 (2006)
  10. Dissecting substrate recognition by thrombin using the inactive mutant S195A. Krem MM, Di Cera E. Biophys. Chem. 100 315-323 (2003)
  11. Estimating binding affinities by docking/scoring methods using variable protonation states. Park MS, Gao C, Stern HA. Proteins 79 304-314 (2011)
  12. Exploration of the P6/P7 region of the peptide-binding site of the human class II major histocompatability complex protein HLA-DR1. Zavala-Ruiz Z, Sundberg EJ, Stone JD, DeOliveira DB, Chan IC, Svendsen J, Mariuzza RA, Stern LJ. J Biol Chem 278 44904-44912 (2003)
  13. Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase. Steuber H, Czodrowski P, Sotriffer CA, Klebe G. J. Mol. Biol. 373 1305-1320 (2007)
  14. A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes. Singh N, Warshel A. Proteins 78 1724-1735 (2010)
  15. Conformational variability of benzamidinium-based inhibitors. Li X, He X, Wang B, Merz K. J. Am. Chem. Soc. 131 7742-7754 (2009)
  16. Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin. Baum B, Muley L, Heine A, Smolinski M, Hangauer D, Klebe G. J. Mol. Biol. 391 552-564 (2009)
  17. Thrombin inhibitors identified by computer-assisted multiparameter design. Riester D, Wirsching F, Salinas G, Keller M, Gebinoga M, Kamphausen S, Merkwirth C, Goetz R, Wiesenfeldt M, Stürzebecher J, Bode W, Friedrich R, Thürk M, Schwienhorst A. Proc. Natl. Acad. Sci. U.S.A. 102 8597-8602 (2005)
  18. A network-based multi-target computational estimation scheme for anticoagulant activities of compounds. Li Q, Li X, Li C, Chen L, Song J, Tang Y, Xu X. PLoS ONE 6 e14774 (2011)
  19. Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features. Steuber H, Heine A, Podjarny A, Klebe G. J. Mol. Biol. 379 991-1016 (2008)
  20. Predicting accurate absolute binding energies in aqueous solution: thermodynamic considerations for electronic structure methods. Jensen JH. Phys Chem Chem Phys 17 12441-12451 (2015)
  21. S1 subsite in snake venom thrombin-like enzymes: can S1 subsite lipophilicity be used to sort binding affinities of trypsin-like enzymes to small-molecule inhibitors? Silva FP, De-Simone SG. Bioorg. Med. Chem. 12 2571-2587 (2004)
  22. From activity cliffs to target-specific scoring models and pharmacophore hypotheses. Seebeck B, Wagener M, Rarey M. ChemMedChem 6 1630-9, 1533 (2011)
  23. High-throughput fragment screening by affinity LC-MS. Duong-Thi MD, Bergström M, Fex T, Isaksson R, Ohlson S. J Biomol Screen 18 160-171 (2013)
  24. ZZ made EZ: influence of inhibitor configuration on enzyme selectivity. Rauh D, Klebe G, Stürzebecher J, Stubbs MT. J. Mol. Biol. 330 761-770 (2003)
  25. Active site mapping of trypsin, thrombin and matriptase-2 by sulfamoyl benzamidines. Dosa S, Stirnberg M, Lülsdorff V, Häußler D, Maurer E, Gütschow M. Bioorg. Med. Chem. 20 6489-6505 (2012)
  26. Comparative binding energy analysis for binding affinity and target selectivity prediction. Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Proteins 78 135-153 (2010)
  27. Profiling the structural determinants for the selectivity of representative factor-Xa and thrombin inhibitors using combined ligand-based and structure-based approaches. Bhunia SS, Roy KK, Saxena AK. J Chem Inf Model 51 1966-1985 (2011)
  28. The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action. Wahlgren WY, Pál G, Kardos J, Porrogi P, Szenthe B, Patthy A, Gráf L, Katona G. J. Biol. Chem. 286 3587-3596 (2011)
  29. The environment of amide groups in protein-ligand complexes: H-bonds and beyond. Cotesta S, Stahl M. J Mol Model 12 436-444 (2006)
  30. Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons. Gerlach C, Smolinski M, Steuber H, Sotriffer CA, Heine A, Hangauer DG, Klebe G. Angew. Chem. Int. Ed. Engl. 46 8511-8514 (2007)
  31. An efficient computational method for calculating ligand binding affinities. Suenaga A, Okimoto N, Hirano Y, Fukui K. PLoS ONE 7 e42846 (2012)
  32. Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors. Surpateanu G, Iorga BI. J. Comput. Aided Mol. Des. 26 595-601 (2012)
  33. Strategies for assessing proton linkage to bimolecular interactions by global analysis of isothermal titration calorimetry data. Coussens NP, Schuck P, Zhao H. J Chem Thermodyn 52 95-107 (2012)
  34. A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates. Fokkens J, Klebe G. Angew. Chem. Int. Ed. Engl. 45 985-989 (2006)
  35. Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. Benson ML, Faver JC, Ucisik MN, Dashti DS, Zheng Z, Merz KM. J. Comput. Aided Mol. Des. 26 647-659 (2012)
  36. Drug-binding energetics of human α-1-acid glycoprotein assessed by isothermal titration calorimetry and molecular docking simulations. Huang JX, Cooper MA, Baker MA, Azad MA, Nation RL, Li J, Velkov T. J. Mol. Recognit. 25 642-656 (2012)
  37. Poisson-Boltzmann continuum-solvation models: applications to pH-dependent properties of biomolecules. Antosiewicz JM, Shugar D. Mol Biosyst 7 2923-2949 (2011)
  38. Selective 3-amino-2-pyridinone acetamide thrombin inhibitors incorporating weakly basic partially saturated heterobicyclic P1-arginine mimetics. Peterlin-Masic L, Kranjc A, Marinko P, Mlinsek G, Solmajer T, Stegnar M, Kikelj D. Bioorg. Med. Chem. Lett. 13 3171-3176 (2003)
  39. Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice. Lachenmann MJ, Ladbury JE, Qian X, Huang K, Singh R, Weiss MA. Protein Sci. 13 3115-3126 (2004)
  40. Uncertainty in protein-ligand binding constants: asymmetric confidence intervals versus standard errors. Paketurytė V, Petrauskas V, Zubrienė A, Abian O, Bastos M, Chen WY, Moreno MJ, Krainer G, Linkuvienė V, Sedivy A, Velazquez-Campoy A, Williams MA, Matulis D. Eur Biophys J 50 661-670 (2021)
  41. Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation. Cardone A, Bornstein A, Pant HC, Brady M, Sriram R, Hassan SA. J Comput Chem 36 983-995 (2015)
  42. Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction. Bruylants G, Wintjens R, Looze Y, Redfield C, Bartik K. Eur. Biophys. J. 37 11-18 (2007)
  43. Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model. Nicolotti O, Giangreco I, Miscioscia TF, Convertino M, Leonetti F, Pisani L, Carotti A. J. Comput. Aided Mol. Des. 24 117-129 (2010)
  44. Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10. Ruiz FX, Cousido-Siah A, Porté S, Domínguez M, Crespo I, Rechlin C, Mitschler A, de Lera ÁR, Martín MJ, de la Fuente JÁ, Klebe G, Parés X, Farrés J, Podjarny A. ChemMedChem 10 1989-2003 (2015)
  45. Computation of entropy contribution to protein-ligand binding free energy. Grigoriev FV, Luschekina SV, Romanov AN, Sulimov VB, Nikitina EA. Biochemistry Mosc. 72 785-792 (2007)
  46. Structure of a novel thrombin inhibitor with an uncharged D-amino acid as P1 residue. Friedrich R, Riester D, Göttig P, Thürk M, Schwienhorst A, Bode W. Eur J Med Chem 43 1330-1335 (2008)
  47. The role of Tyr71 in Streptomyces trypsin on the recognition mechanism of structural protein substrates. Uesugi Y, Usuki H, Iwabuchi M, Hatanaka T. FEBS J. 276 5634-5646 (2009)
  48. Thrombin inhibitors with novel P1 binding pocket functionality: free energy of binding analysis. Mlinsek G, Oblak M, Hodoscek M, Solmajer T. J Mol Model 13 247-254 (2007)
  49. Beyond heparinization: design of highly potent thrombin inhibitors suitable for surface coupling. Steinmetzer T, Baum B, Biela A, Klebe G, Nowak G, Bucha E. ChemMedChem 7 1965-1973 (2012)
  50. Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin. Mashima A, Kurahashi M, Sasahara K, Yoshida T, Chuman H. Mol Inform 33 802-814 (2014)
  51. Interaction of Cu(2+), Pb (2+), Zn (2+) with trypsin: what is the key factor of their toxicity? Zhang T, Zhang H, Liu G, Gao C, Liu R. J Fluoresc 24 1803-1810 (2014)
  52. KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding. Gerlach C, Münzel M, Baum B, Gerber HD, Craan T, Diederich WE, Klebe G. Angew. Chem. Int. Ed. Engl. 46 9105-9109 (2007)
  53. Lead identification in post-genomics: computers as a complementary alternative. Klebe G. Drug Discov Today Technol 1 225-230 (2004)
  54. A Bisbenzamidine Phosphonate as a Janus-faced Inhibitor for Trypsin-like Serine Proteases. Häußler D, Scheidt T, Stirnberg M, Steinmetzer T, Gütschow M. ChemMedChem 10 1641-1646 (2015)
  55. A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level. Horváth I, Jeszenői N, Bálint M, Paragi G, Hetényi C. Int J Mol Sci 20 (2019)
  56. Investigation of trypsin-CdSe quantum dot interactions via spectroscopic methods and effects on enzymatic activity. Kaur G, Tripathi SK. Spectrochim Acta A Mol Biomol Spectrosc 134 173-183 (2015)
  57. Modulating Conformational Preferences by Allylic Strain toward Improved Physical Properties and Binding Interactions. Zhao H. ACS Omega 7 9080-9085 (2022)
  58. Weak affinity chromatography for evaluation of stereoisomers in early drug discovery. Duong-Thi MD, Bergström M, Fex T, Svensson S, Ohlson S, Isaksson R. J Biomol Screen 18 748-755 (2013)


Related citations provided by authors (3)

  1. Structural and Functional Analyses of Benzamidine-Based Inhibitors in Complex with Trypsin: Implications for the Inhibition of Factor Xa, Tpa, and Urokinase. Renatus M, Bode W, Huber R, Stuerzebecher J, Stubbs MT J. Med. Chem. 41 5445-5456 (1998)
  2. Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin. Stubbs MT, Huber R, Bode W FEBS Lett. 375 103-107 (1995)
  3. A Player of Many Parts: The Spotlight Falls on Thrombin'S Structure. Stubbs MT, Bode W Thromb. Res. 69 1-58 (1993)

Quick links