Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)

Erik de Heuvel; Abhimanyu K. Singh; Pierre Boronat; Albert J. Kooistra; Tiffany van der Meer; Payman Sadek; Antoni R. Blaazer; Nathan C. Shaner; Daphne S. Bindels; Guy Caljon; Louis Maes; Geert Jan Sterk; Marco Siderius; Michael Oberholzer; Iwan J. P. de Esch; David G. Brown; Rob Leurs

doi:10.1016/j.bmc.2019.06.026

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)

Erik de Heuvel, Abhimanyu K. Singh, Pierre Boronat, Albert J. Kooistra, Tiffany van der Meer, Payman Sadek, Antoni R. Blaazer, Nathan C. Shaner, Daphne S. Bindels, Guy Caljon, Louis Maes, Geert Jan Sterk, Marco Siderius, Michael Oberholzer, Iwan J. P. de Esch, David G. Brown, Rob Leurs

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

Inhibitors against Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) and B2 (TbrPDEB2) have gained interest as new treatments for human African trypanosomiasis. The recently reported alkynamide tetrahydrophthalazinones, which show submicromolar activities against TbrPDEB1 and anti-T. brucei activity, have been used as starting point for the discovery of new TbrPDEB1 inhibitors. Structure-based design indicated that the alkynamide-nitrogen atom can be readily decorated, leading to the discovery of 37, a potent TbrPDEB1 inhibitor with submicromolar activities against T. brucei parasites. Furthermore, 37 is more potent against TbrPDEB1 than hPDE4 and shows no cytotoxicity on human MRC-5 cells. The crystal structures of the catalytic domain of TbrPDEB1 co-crystalized with several different alkynamides show a bidentate interaction with key-residue Gln874, but no interaction with the parasite-specific P-pocket, despite being (uniquely) a more potent inhibitor for the parasite PDE. Incubation of blood stream form trypanosomes by 37 increases intracellular cAMP levels and results in the distortion of the cell cycle and cell death, validating phosphodiesterase inhibition as mode of action.

Original language	English
Pages (from-to)	4013-4029
Number of pages	17
Journal	Bioorganic and Medicinal Chemistry
Volume	27
Issue number	18
DOIs	https://doi.org/10.1016/j.bmc.2019.06.026
Publication status	Published - 15 Sept 2019

Funding

We thank F.G.J. Custers (Vrije Universiteit Amsterdam) for analytical support. We thank Jay Bangs (University at Buffalo) for providing T. brucei brucei culture medium, Viacheslav O. Nikolaev (Universitätsklinikum Hamburg-Eppendorf) for providing the Epac1camps plasmid, Tom Seebeck for the anti-PFR antibody. Funding: This work was supported by the European Commission 7th Framework Programme FP7-HEALTH-2013-INNOVATION-1 under project reference 602666 “Parasite-specific cyclic nucleotide phosphodiesterase inhibitors to target Neglected Parasitic Diseases” (PDE4NPD) and by the European Union’s Horizon2020 MSCA Programme under grant agreement 675899 (FRAGNET). This work was supported in part by grant R01GM109984 to NCS . We thank F.G.J. Custers (Vrije Universiteit Amsterdam) for analytical support. We thank Jay Bangs (University at Buffalo) for providing T. brucei brucei culture medium, Viacheslav O. Nikolaev (Universit?tsklinikum Hamburg-Eppendorf) for providing the Epac1camps plasmid, Tom Seebeck for the anti-PFR antibody. Funding: This work was supported by the European Commission 7th Framework Programme FP7-HEALTH-2013-INNOVATION-1 under project reference 602666 ?Parasite-specific cyclic nucleotide phosphodiesterase inhibitors to target Neglected Parasitic Diseases? (PDE4NPD) and by the European Union's Horizon2020 MSCA Programme under grant agreement 675899 (FRAGNET). This work was supported in part by grant R01GM109984 to NCS. E.d.H. G.J.S. and I.J.P.d.E. were involved in compound design, synthesis and analysis. A.K.S. and D.G.B. were involved in protein production, crystallization, data collection and refinement for structural studies. E.d.H. A.K.S. and D.G.B. were involved in crystal structure analysis. E.d.H. and A.J.K. were involved in virtual screening and docking. T.v.d.M. P.S. and M.S. were involved in the biochemical assays. G.C. and L.M. were involved in the phenotypic cellular assays. P.B. and A.R.B. were involved in SPR analysis. M.O. NS and DB were involved in the target validation experiments. L.M. G.J.S. I.J.P.d.E. D.G.B. and R.L. supervised the experiments and conceived the project. E.d.H. A.K.S. G.J.S. I.J.P.d.E. and R.L. integrated all data and wrote the manuscript.

Funders	Funder number
European Commission 7th Framework Programme FP7-HEALTH-2013-INNOVATION-1	PDE4NPD
European Union's Horizon2020 MSCA
European Union’s Horizon2020 MSCA	675899, R01GM109984
Universit?tsklinikum Hamburg-Eppendorf
Seventh Framework Programme	602666

Keywords

Trypanosoma brucei phosphodiesterase B1
Enzyme inhibitors
Neglected tropical disease
Human African trypanosomiasis
Structure-based drug discovery
Fluorescence microscopy

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.bmc.2019.06.026

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de Heuvel, E., Singh, A. K., Boronat, P., Kooistra, A. J., van der Meer, T., Sadek, P., Blaazer, A. R., Shaner, N. C., Bindels, D. S., Caljon, G., Maes, L., Sterk, G. J., Siderius, M., Oberholzer, M., de Esch, I. J. P., Brown, D. G., & Leurs, R. (2019). Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2). Bioorganic and Medicinal Chemistry, 27(18), 4013-4029. https://doi.org/10.1016/j.bmc.2019.06.026

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title = "Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)",

abstract = "Inhibitors against Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) and B2 (TbrPDEB2) have gained interest as new treatments for human African trypanosomiasis. The recently reported alkynamide tetrahydrophthalazinones, which show submicromolar activities against TbrPDEB1 and anti-T. brucei activity, have been used as starting point for the discovery of new TbrPDEB1 inhibitors. Structure-based design indicated that the alkynamide-nitrogen atom can be readily decorated, leading to the discovery of 37, a potent TbrPDEB1 inhibitor with submicromolar activities against T. brucei parasites. Furthermore, 37 is more potent against TbrPDEB1 than hPDE4 and shows no cytotoxicity on human MRC-5 cells. The crystal structures of the catalytic domain of TbrPDEB1 co-crystalized with several different alkynamides show a bidentate interaction with key-residue Gln874, but no interaction with the parasite-specific P-pocket, despite being (uniquely) a more potent inhibitor for the parasite PDE. Incubation of blood stream form trypanosomes by 37 increases intracellular cAMP levels and results in the distortion of the cell cycle and cell death, validating phosphodiesterase inhibition as mode of action.",

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de Heuvel, E, Singh, AK, Boronat, P, Kooistra, AJ, van der Meer, T, Sadek, P, Blaazer, AR, Shaner, NC, Bindels, DS, Caljon, G, Maes, L, Sterk, GJ, Siderius, M, Oberholzer, M, de Esch, IJP, Brown, DG & Leurs, R 2019, 'Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)', Bioorganic and Medicinal Chemistry, vol. 27, no. 18, pp. 4013-4029. https://doi.org/10.1016/j.bmc.2019.06.026

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T1 - Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)

AU - de Heuvel, Erik

AU - Singh, Abhimanyu K.

AU - Boronat, Pierre

AU - Kooistra, Albert J.

AU - van der Meer, Tiffany

AU - Sadek, Payman

AU - Blaazer, Antoni R.

AU - Shaner, Nathan C.

AU - Bindels, Daphne S.

AU - Caljon, Guy

AU - Maes, Louis

AU - Sterk, Geert Jan

AU - Siderius, Marco

AU - Oberholzer, Michael

AU - de Esch, Iwan J. P.

AU - Brown, David G.

AU - Leurs, Rob

PY - 2019/9/15

Y1 - 2019/9/15

N2 - Inhibitors against Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) and B2 (TbrPDEB2) have gained interest as new treatments for human African trypanosomiasis. The recently reported alkynamide tetrahydrophthalazinones, which show submicromolar activities against TbrPDEB1 and anti-T. brucei activity, have been used as starting point for the discovery of new TbrPDEB1 inhibitors. Structure-based design indicated that the alkynamide-nitrogen atom can be readily decorated, leading to the discovery of 37, a potent TbrPDEB1 inhibitor with submicromolar activities against T. brucei parasites. Furthermore, 37 is more potent against TbrPDEB1 than hPDE4 and shows no cytotoxicity on human MRC-5 cells. The crystal structures of the catalytic domain of TbrPDEB1 co-crystalized with several different alkynamides show a bidentate interaction with key-residue Gln874, but no interaction with the parasite-specific P-pocket, despite being (uniquely) a more potent inhibitor for the parasite PDE. Incubation of blood stream form trypanosomes by 37 increases intracellular cAMP levels and results in the distortion of the cell cycle and cell death, validating phosphodiesterase inhibition as mode of action.

AB - Inhibitors against Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) and B2 (TbrPDEB2) have gained interest as new treatments for human African trypanosomiasis. The recently reported alkynamide tetrahydrophthalazinones, which show submicromolar activities against TbrPDEB1 and anti-T. brucei activity, have been used as starting point for the discovery of new TbrPDEB1 inhibitors. Structure-based design indicated that the alkynamide-nitrogen atom can be readily decorated, leading to the discovery of 37, a potent TbrPDEB1 inhibitor with submicromolar activities against T. brucei parasites. Furthermore, 37 is more potent against TbrPDEB1 than hPDE4 and shows no cytotoxicity on human MRC-5 cells. The crystal structures of the catalytic domain of TbrPDEB1 co-crystalized with several different alkynamides show a bidentate interaction with key-residue Gln874, but no interaction with the parasite-specific P-pocket, despite being (uniquely) a more potent inhibitor for the parasite PDE. Incubation of blood stream form trypanosomes by 37 increases intracellular cAMP levels and results in the distortion of the cell cycle and cell death, validating phosphodiesterase inhibition as mode of action.

KW - Trypanosoma brucei phosphodiesterase B1

KW - Enzyme inhibitors

KW - Neglected tropical disease

KW - Human African trypanosomiasis

KW - Structure-based drug discovery

KW - Fluorescence microscopy

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JO - Bioorganic and Medicinal Chemistry

JF - Bioorganic and Medicinal Chemistry

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Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)

Abstract

Funding

Keywords

UN SDGs

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Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors

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