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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  6. Identification of Chemical Profiles and Biological Properties of Rhizophora racemosa G. Mey. Extracts Obtained by Different Methods and Solvents. Chiavaroli A, Sinan KI, Zengin G, Mahomoodally MF, Sadeer NB, Etienne OK, Cziáky Z, Jekő J, Glamocilja J, Sokovic M, Recinella L, Brunetti L, Leone S, Abdullah HH, Angelini P, Flores GA, Venanzoni R, Menghini L, Orlando G, Ferrante C. Antioxidants (Basel) 9 E533 (2020)
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  8. Macrophage Migration Inhibitory Factor Acts as the Potential Target of a Newly Synthesized Compound, 1-(9'-methyl-3'-carbazole)-3, 4-dihydro-β-carboline. Ko PH, Shen YC, Murugan K, Huang CW, Sivakumar G, Pal P, Liao CC, Luo KS, Chuang EY, Tsai MH, Lai LC. Sci Rep 9 2147 (2019)
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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)
  10. Ligand binding to nucleic acids and proteins: Does selectivity increase with strength? Schneider HJ. Eur J Med Chem 43 2307-2315 (2008)
  11. Spatial mismatch, non-additive binding energies and selectivity in supramolecular complexes. Schneider HJ. Org Biomol Chem 15 2146-2151 (2017)

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