Molecular Interactions between Acetylpolymine-aminohydrolases of Pseudomonas aeruginosa and small organic Ligands

• Applicant: Professor Dr. Franz-Josef Meyer-Almes
• Subject Area: Pharmacy ; Biological and Biomimetic Chemistry
• Term: from 2013 to 2016
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 236178355

• Final Report Year: 2016

Final Report Abstract

Our findings significantly extend existing knowledge about the physiological function, 3D-structure, dimer formation and substrate specificity of HDAC like enzymes in the human pathogen P. aeruginosa. Moreover, a combined thermodynamic, kinetic and structural study of native and mutated proteins revealed new insights into the relationship between flexibility by the example of the L2 loop and the mechanism and thermodynamic signature of ligand binding. These scientific findings certainly contribute to a deeper understanding of the molecular interaction between HDAC like enzymes to form distinct dimers as well as between these enzymes and ligands. Since HDACs are prominent pharmaceutical targets, the gained knowledge resulting from this study is supposed to serve as a valuable guide for the design and optimization of new drug candidates with improved selectivity. The present project concentrates mainly on the APAHs of P. aeruginosa, but also spreads out to human HDACs if one looks at the selective HDAC8 inhibitor found in the screening campaign. In contrast to the suggested antiinfective drug targets APAHs, human HDACs are well established pharmaceutical targets and particularly selective inhibitors earn special attention. The identified class of HDAC8 selective inhibitors without any known zinc binding motif and unknown mode of action with the preferred target HDAC8 deserve more attention. It would be interesting to learn more about the structure-activity but also structure-binding kinetics relationship of this compound and derivatives thereof. The mechanism of the already observed activity on cancer cells has also to be elucidated in more detail to learn about improved follow-up compounds. To mention one aspect: it has to be investigated, whether or to which extend these compounds are transformed in the respective thiophenol and interfere with reduction equivalents within cells.

Publications

• A fluorescence lifetime-based binding assay for acetylpolyamine amidohydrolases from Pseudomonas aeruginosa using a [1,3]dioxolo[4,5-f][1,3]benzodioxole (DBD) ligand probe. Anal Bioanal Chem. 2014 Aug;406(20):4889-97
  Meyners C, Wawrzinek R, Krämer A, Hinz S, Wessig P, Meyer-Almes FJ
  
• Kinetic binding assays for the analysis of protein-ligand interactions. Drug Discov Today Technol. 2015 Oct;17:1-8
  Meyer-Almes FJ
  
• Crystal structure of a histone deacetylase homologue from Pseudomonas aeruginosa. Biochemistry, 2016, 55 (49), pp 6858–6868
  Krämer A, Wagner T, Yildiz Ö, Meyer-Almes FJ
  
• Discrimination between conformational selection and induced fit protein-ligand binding using Integrated Global Fit analysis. Eur Biophys J. 2016 Apr;45(3):245-57
  Meyer-Almes FJ
  
• Potent and Selective Non‐hydroxamate Histone Deacetylase 8 Inhibitors. ChemMedChem, 11,23, December 6, 2016, Pages 2598-2606
  Kleinschek A, Meyners C, Digiorgio E, Brancolini C, Meyer-Almes FJ
  
• Substrate specificity and function of acetylpolyamine amidohydrolases from Pseudomonas aeruginosa. BMC Biochem. 2016 Mar 9;17:4
  Krämer A, Herzer J, Overhage J, Meyer-Almes FJ
  
• The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket. Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1861, Issue 7, July 2017, Pages 1855-1863
  Meyners C, Krämer A, Yiliz Ö, Meyer-Almes FJ
  
• Towards photopharmacological antimicrobial chemotherapy using photoswitchable amidohydrolase inhibitors. ACS Infectious Diseases, 2017, 3 (2), pp 152–161
  Weston CE, Krämer A, Colin F, Yildiz Ö, Baud MGJ, Meyer-Almes FJ, Fuchter MJ