3f17 › Citations

Exploring the subtleties of drug-receptor interactions: the case of matrix metalloproteinases.

Bertini I, Calderone V, Fragai M, Giachetti A, Loconte M, Luchinat C, Maletta M, Nativi C, Yeo KJ
J Am Chem Soc 129 2466-75 (2007)
Related entries: 1os2, 1os9, 3f15, 3f16, 3f18, 3f19, 3f1a, 3lk8, 3nx7

Cited: 42 times
EuropePMC logo PMID: 17269766

Abstract

By solving high-resolution crystal structures of a large number (14 in this case) of adducts of matrix metalloproteinase 12 (MMP12) with strong, nanomolar, inhibitors all derived from a single ligand scaffold, it is shown that the energetics of the ligand-protein interactions can be accounted for directly from the structures to a level of detail that allows us to rationalize for the differential binding affinity between pairs of closely related ligands. In each case, variations in binding affinities can be traced back to slight improvements or worsening of specific interactions with the protein of one or more ligand atoms. Isothermal calorimetry measurements show that the binding of this class of MMP inhibitors is largely enthalpy driven, but a favorable entropic contribution is always present. The binding enthalpy of acetohydroxamic acid (AHA), the prototype zinc-binding group in MMP drug discovery, has been also accurately measured. In principle, this research permits the planning of either improved inhibitors, or inhibitors with improved selectivity for one or another MMP. The present analysis is applicable to any drug target for which structural information on adducts with a series of homologous ligands can be obtained, while structural information obtained from in silico docking is probably not accurate enough for this type of study.

Articles - 3f17 mentioned but not cited (11)

  1. The essential protein for bacterial flagella formation FlgJ functions as a β-N-acetylglucosaminidase. Herlihey FA, Moynihan PJ, Clarke AJ. J Biol Chem 289 31029-31042 (2014)
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Reviews citing this publication (11)

  1. Perspectives on NMR in drug discovery: a technique comes of age. Pellecchia M, Bertini I, Cowburn D, Dalvit C, Giralt E, Jahnke W, James TL, Homans SW, Kessler H, Luchinat C, Meyer B, Oschkinat H, Peng J, Schwalbe H, Siegal G. Nat Rev Drug Discov 7 738-745 (2008)
  2. Metalloproteinases and Their Inhibitors: Potential for the Development of New Therapeutics. Raeeszadeh-Sarmazdeh M, Do LD, Hritz BG. Cells 9 E1313 (2020)
  3. Matrix metalloproteinases as breast cancer drivers and therapeutic targets. Radisky ES, Radisky DC. Front Biosci (Landmark Ed) 20 1144-1163 (2015)
  4. A look at ligand binding thermodynamics in drug discovery. Claveria-Gimeno R, Vega S, Abian O, Velazquez-Campoy A. Expert Opin Drug Discov 12 363-377 (2017)
  5. A survey of the year 2007 literature on applications of isothermal titration calorimetry. Bjelić S, Jelesarov I. J Mol Recognit 21 289-312 (2008)
  6. Recent trends and some applications of isothermal titration calorimetry in biotechnology. Roselin LS, Lin MS, Lin PH, Chang Y, Chen WY. Biotechnol J 5 85-98 (2010)
  7. Mechanism-based profiling of MMPs. Fisher JF, Mobashery S. Methods Mol Biol 622 471-487 (2010)
  8. Is there a link between selectivity and binding thermodynamics profiles? Tarcsay Á, Keserű GM. Drug Discov Today 20 86-94 (2015)
  9. Arylsulfonamides and selectivity of matrix metalloproteinase-2: An overview. Adhikari N, Mukherjee A, Saha A, Jha T. Eur J Med Chem 129 72-109 (2017)
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  11. Spatial mismatch, non-additive binding energies and selectivity in supramolecular complexes. Schneider HJ. Org Biomol Chem 15 2146-2151 (2017)

Articles citing this publication (20)

  1. MMP-12 catalytic domain recognizes triple helical peptide models of collagen V with exosites and high activity. Bhaskaran R, Palmier MO, Lauer-Fields JL, Fields GB, Van Doren SR. J Biol Chem 283 21779-21788 (2008)
  2. Molecular docking and inhibition of matrix metalloproteinase-2 by novel difluorinatedbenzylidene curcumin analog. Ahmad A, Sayed A, Ginnebaugh KR, Sharma V, Suri A, Saraph A, Padhye S, Sarkar FH. Am J Transl Res 7 298-308 (2015)
  3. Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors. Alcaraz LA, Banci L, Bertini I, Cantini F, Donaire A, Gonnelli L. J Biol Inorg Chem 12 1197-1206 (2007)
  4. SSNMR of biosilica-entrapped enzymes permits an easy assessment of preservation of native conformation in atomic detail. Fragai M, Luchinat C, Martelli T, Ravera E, Sagi I, Solomonov I, Udi Y. Chem Commun (Camb) 50 421-423 (2014)
  5. A highly soluble matrix metalloproteinase-9 inhibitor for potential treatment of dry eye syndrome. Mori M, De Lorenzo E, Torre E, Fragai M, Nativi C, Luchinat C, Arcangeli A. Basic Clin Pharmacol Toxicol 111 289-295 (2012)
  6. An integrated computational and experimental approach to gaining selectivity for MMP-2 within the gelatinase subfamily. Fabre B, Filipiak K, Díaz N, Zapico JM, Suárez D, Ramos A, de Pascual-Teresa B. Chembiochem 15 399-412 (2014)
  7. Potent "clicked" MMP2 inhibitors: synthesis, molecular modeling and biological exploration. Zapico JM, Serra P, García-Sanmartín J, Filipiak K, Carbajo RJ, Schott AK, Pineda-Lucena A, Martínez A, Martín-Santamaría S, de Pascual-Teresa B, Ramos A. Org Biomol Chem 9 4587-4599 (2011)
  8. Catalytic domain of MMP20 (Enamelysin) - the NMR structure of a new matrix metalloproteinase. Arendt Y, Banci L, Bertini I, Cantini F, Cozzi R, Del Conte R, Gonnelli L. FEBS Lett 581 4723-4726 (2007)
  9. Discovery of a New Class of Potent MMP Inhibitors by Structure-Based Optimization of the Arylsulfonamide Scaffold. Mori M, Massaro A, Calderone V, Fragai M, Luchinat C, Mordini A. ACS Med Chem Lett 4 565-569 (2013)
  10. A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations. Hitaoka S, Chuman H, Yoshizawa K. Org Biomol Chem 13 793-806 (2015)
  11. A macrophage cell model for selective metalloproteinase inhibitor design. Jacobsen FE, Buczynski MW, Dennis EA, Cohen SM. Chembiochem 9 2087-2095 (2008)
  12. Targeting matrix metalloproteinases: design of a bifunctional inhibitor for presentation by tumour-associated galectins. Bartoloni M, Domínguez BE, Dragoni E, Richichi B, Fragai M, André S, Gabius HJ, Ardá A, Luchinat C, Jiménez-Barbero J, Nativi C. Chemistry 19 1896-1902 (2013)
  13. 2-Benzisothiazolylimino-5-benzylidene-4-thiazolidinones as protective agents against cartilage destruction. Crascì L, Vicini P, Incerti M, Cardile V, Avondo S, Panico A. Bioorg Med Chem 23 1551-1556 (2015)
  14. In silico study of MMP inhibition. Rouffet M, Denhez C, Bourguet E, Bohr F, Guillaume D. Org Biomol Chem 7 3817-3825 (2009)
  15. Benzisothiazolyliminothiazolidin-4-ones with chondroprotective properties: searching for potent and selective inhibitors of MMP-13. Vicini P, Crascì L, Incerti M, Ronsisvalle S, Cardile V, Panico AM. ChemMedChem 6 1199-1202 (2011)
  16. Probing water-protein contacts in a MMP-12/CGS27023A complex by nuclear magnetic resonance spectroscopy. Kovacs H, Agback T, Isaksson J. J Biomol NMR 53 85-92 (2012)
  17. Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. Yokoyama H, Sawada JI, Sato K, Ogo N, Kamei N, Ishikawa Y, Hara K, Asai A, Hashimoto H. ACS Omega 3 12284-12294 (2018)
  18. Synthesis and binding monitoring of a new nanomolar PAMAM-based matrix metalloproteinases inhibitor (MMPIs). Cerofolini L, Baldoneschi V, Dragoni E, Storai A, Mamusa M, Berti D, Fragai M, Richichi B, Nativi C. Bioorg Med Chem 25 523-527 (2017)
  19. The heat is on: thermodynamic analysis in fragment-based drug discovery. Drug Discov Today Technol 7 e147-202 (2010)
  20. Functionalized Hyaluronic Acid for "In Situ" Matrix Metalloproteinase Inhibition: A Bioactive Material to Treat the Dry Eye Sydrome. Burgalassi S, Fragai M, Francesconi O, Cerofolini L, Monti D, Leone G, Lamponi S, Greco G, Magnani A, Nativi C. ACS Macro Lett 11 1190-1194 (2022)


Related citations provided by authors (1)

  1. X-ray structures of binary and ternary enzyme-product-inhibitor complexes of matrix metalloproteinases.. Bertini I, Calderone V, Fragai M, Luchinat C, Mangani S, Terni B Angew Chem Int Ed Engl 42 2673-6 (2003)

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