Mapping the S1 and S1' subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents

Lorenzo Cianni; Carina Lemke; Erik Gilberg; Christian Feldmann; Fabiana Rosini; Fernanda Dos Reis Rocho; Jean F R Ribeiro; Daiane Y Tezuka; Carla D Lopes; Sérgio de Albuquerque; Jürgen Bajorath; Stefan Laufer; Andrei Leitão; Michael Gütschow; Carlos A Montanari

doi:10.1371/journal.pntd.0007755

Mapping the S1 and S1' subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents

PLoS Negl Trop Dis. 2020 Mar 12;14(3):e0007755. doi: 10.1371/journal.pntd.0007755. eCollection 2020 Mar.

Authors

Lorenzo Cianni^{1

2

3

4}, Carina Lemke², Erik Gilberg^{2

3}, Christian Feldmann³, Fabiana Rosini¹, Fernanda Dos Reis Rocho¹, Jean F R Ribeiro¹, Daiane Y Tezuka^{1

5}, Carla D Lopes⁶, Sérgio de Albuquerque⁶, Jürgen Bajorath³, Stefan Laufer⁴, Andrei Leitão¹, Michael Gütschow², Carlos A Montanari¹

Affiliations

¹ Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil.
² Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, Bonn, Germany.
³ Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany.
⁴ Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Tübingen, Germany.
⁵ Ribeirão Preto School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
⁶ Department of Clinical Toxicological and Bromatological Analysis School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil.

Abstract

The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. A series of 26 new compounds were designed, synthesized, and tested against the recombinant cruzain (Cz) to map its S1/S1´ subsites. The same series was evaluated on a panel of four human cysteine proteases (CatB, CatK, CatL, CatS) and Leishmania mexicana CPB, which is a potential target for the treatment of cutaneous leishmaniasis. The synthesized compounds are dipeptidyl nitriles designed based on the most promising combinations of different moieties in P1 (ten), P2 (six), and P3 (four different building blocks). Eight compounds exhibited a Ki smaller than 20.0 nM for Cz, whereas three compounds met these criteria for LmCPB. Three inhibitors had an EC50 value of ca. 4.0 μM, thus being equipotent to benznidazole according to the antitrypanosomal effects. Our mapping approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cysteine proteases.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cysteine Endopeptidases
Cysteine Proteases / metabolism
Cysteine Proteinase Inhibitors / pharmacology*
Dipeptides / pharmacology*
Humans
Leishmania mexicana / enzymology*
Nitriles / pharmacology*
Protozoan Proteins / antagonists & inhibitors*
Trypanocidal Agents / pharmacology*
Trypanosoma cruzi / enzymology*

Substances

Cysteine Proteinase Inhibitors
Dipeptides
Nitriles
Protozoan Proteins
Trypanocidal Agents
Cysteine Proteases
Cysteine Endopeptidases
cruzipain

Grants and funding

We are indebted to Fundação de Amparo à Pesquisa do Estado de São Paulo – FAPESP (grant #2013/18009-4, grant #2016/07946-5 and grant #2017/17386-0) for financing this project. We also want to acknowledge the National Council for Scientific and Technological Development (CNPq, grant # 304030/2018-0) in Brazil for scholarships. We would also like to thank the CAPES Drug Discovery program (Process #139/2015) that allowed us to evaluate LmCPB inhibitors. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.