Structure-based design of multi-target drugs using the example of dual inhibitors of LTA4 hydrolase and soluble epoxide hydrolase
Final Report Abstract
Design of multi-target drugs became an emerging field in medicinal chemistry. Multi-target ligands often exhibit an improved efficacy compared to single-target agents and are safer than a combination of multiple drugs. The development of multi-target drugs can be more challenging in comparison to a single-acting ligand because of the more complex design process. The optimization of physicochemical and pharmacokinetic properties regarding more than one target simultaneously requires an efficient and rational design strategy and led to new approaches in the fields of medicinal and computational chemistry. This project deals with design, synthesis and in vitro evaluation of dual inhibitors of soluble epoxide hydrolase (sEH) and leukotriene A4 hydrolase (LTA4H). In this project we developed efficient strategies to find novel starting points for the design of multi-target ligands. We demonstrated that chemical fragments with low molecular weight which bind to both enzymes could be found by screening a medium-size fragment library by means of Differential Scanning Fluorimetry (DSF) as a robust and broadly applicable screening technique. General applicability of DSF screening was shown for five different proteins: sEH, LTA4H, 5-lipoxygenase, retinoid X receptor α, and farnesoid X receptor. In six out of ten cases, dual target fragments could be identified. The mediocre hit rate leads to the assumption that larger screening libraries, or lower activity thresholds are more suitable for identification of dual binding fragments. Potency optimization by fragment growing was in the focus of the second project part. We developed a ligand- and a structure-based in silico technique to identify suitable fragment extensions from a combinatorial library. For the ligand-based fragment growing, Random Forest classifier was used to train two predictors of potential activity towards sEH and LTA4H based on active compounds from ChEMBL database and random inactive molecules. The structure-based technique relied on protein-ligand interaction fingerprints (PLIFs), derived from published X-ray structures of both enzymes. Subsequent docking of the combinatorial library and machine learning based scoring led to prediction of dual ligands. Most promising compounds suggested by both, ligand- and a structurebased approaches were synthesized and evaluated in vitro, yielding potent dual sEH/LTA4H inhibitors. In parallel, rational fragment growing based on literature was applied to design a prototype dual sEH/LTA4H inhibitor with sub-micromolar activity towards both targets. Preliminary structure-activity relationship studies were performed to identify optimal substitution patterns. X-ray structure analysis of a promising dual inhibitor in complex with sEH, as well as molecular docking with LTA4H provided suggestions for further optimization. Hereby, scaffold extension was successfully applied to yield potent dual sEH/LTA4H inhibitors. The spectrum of pro- and anti-inflammatory lipid mediators was evaluated in M1 and M2 macrophages, stimulated with LPS and incubated with the most promising compound, qualifying dual sEH/LTA4H inhibitors as an interesting option for future evaluation as anti-inflammatory agents.
Publications
- (2017) A Dual Modulator of Farnesoid X Receptor and Soluble Epoxide Hydrolase To Counter Nonalcoholic Steatohepatitis. J. Med. Chem. 60, 7703-7724
Schmidt, J., Rotter, M., Weiser, T., Wittmann, S.W., Weizel. L., Kaiser, A., Heering, J., Goebel, T., Angioni, C., Wurglics, M., Paulke, A., Geisslinger, G., Kahnt, A., Steinhilber, D., Proschak, E., Merk, D.
(See online at https://doi.org/10.1021/acs.jmedchem.7b01804) - (2018) Orally available soluble epoxide hydrolase/phosphodiesterase 4 dual inhibitor treats inflammatory pain. J. Med. Chem. 61, 3541-3550
Blöcher, R., Wagner, K.M., Gopireddy, R.R., Harris, T.R., Wu, H., Barnych, B., Hwang, S.H., Xiang, Y.K., Proschak, E., Morisseau, C., Hammock, B.D.
(See online at https://doi.org/10.1021/acs.jmedchem.7b01804) - (2019) Computer-Aided Selective Optimization of Side Activities of Talinolol. ACS Med. Chem. Lett. 10; 899-903
Hiesinger, K., Kramer, J.S., Achenbach, J., Moser, D., Weber, J., Wittmann, S.K., Morisseau, C., Angioni, C., Geisslinger, G., Kahnt, A.S., Kaiser, A., Proschak, A., Steinhilber, D., Pogoryelov, D., Wagner, K., Hammock, B.D., Proschak, E.
(See online at https://doi.org/10.1021/acsmedchemlett.9b00075) - (2019) Development of multitarget agents possessing soluble epoxide hydrolase inhibitory activity. Prostaglandins Other Lipid Mediat. 140, 31-39
Hiesinger, K., Wagner, K.M., Hammock, B.D., Proschak, E., Hwang, S.H.
(See online at https://doi.org/10.1016/j.prostaglandins.2018.12.003) - (2019) Polypharmacology by Design: A Medicinal Chemist's Perspective on Multitargeting Compounds. J. Med. Chem. 62; 420-444
Proschak, E., Stark, H., Merk, D.
(See online at https://doi.org/10.1021/acs.jmedchem.8b00760) - (2019) Zafirlukast is a dual modulator of human soluble epoxide hydrolase and PPARgamma. Front. Pharmacol. 10:263
Göbel, T., Diehl, O., Wittmann, S.K., Merk, D., Angioni, C., Buscató, E., Kottke, R., Heering, J., Weizel, L., Schader, T., Maier, T.J., Geisslinger, G., Schubert-Zsilavecz, M., Steinhilber, D., Proschak, E., Kahnt, A.S.
(See online at https://doi.org/10.3389/fphar.2019.00263)
