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Iacobucci I, Monaco V, Hovasse A, Dupouy B, Keumoe R, Cichocki B, Elhabiri M, Meunier B, Strub JM, Monti M, Cianférani S, Blandin SA, Schaeffer-Reiss C, Davioud-Charvet E. Proteomic Profiling of Antimalarial Plasmodione Using 3-Benz(o)ylmenadione Affinity-Based Probes. Chembiochem 2024; 25:e202400187. [PMID: 38639212 DOI: 10.1002/cbic.202400187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024]
Abstract
Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells. To elucidate its molecular mechanisms, an affinity-based protein profiling (AfBPP) approach was applied to yeast and P. falciparum proteomes. New (pro-) AfBPP probes based on the 3-benz(o)yl-6-fluoro-menadione scaffold were synthesized. With optimized conditions of both photoaffinity labeling and click reaction steps, the AfBPP protocol was then applied to a yeast proteome, yielding 11 putative drug-protein targets. Among these, we found four proteins associated with oxidoreductase activities, the hypothesized type of targets for plasmodione and its metabolites, and other proteins associated with the mitochondria. In Plasmodium parasites, the MS analysis revealed 44 potential plasmodione targets that need to be validated in further studies. Finally, the localization of a 3-benzyl-6-fluoromenadione AfBPP probe was studied in the subcellular structures of the parasite at the trophozoite stage.
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Affiliation(s)
- Ilaria Iacobucci
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Vittoria Monaco
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Baptiste Dupouy
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Rodrigue Keumoe
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Bogdan Cichocki
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Mourad Elhabiri
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-Sur-Yvette Cedex, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant' Angelo, Via Cintia 26, I-80126, Napoli, Italy
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Stéphanie A Blandin
- Institut de Biologie Moléculaire et Cellulaire, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, 2, Allée Konrad Roentgen, -67084, Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178 CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, F-67087, Strasbourg, France
| | - Elisabeth Davioud-Charvet
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic & Medicinal Chemistry, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, 25, rue Becquerel, F-67087, Strasbourg, France
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2
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Trometer N, Pecourneau J, Feng L, Navarro-Huerta JA, Lazarin-Bidóia D, de Oliveira Silva Lautenschlager S, Maes L, Fortes Francisco A, Kelly JM, Meunier B, Cal M, Mäser P, Kaiser M, Davioud-Charvet E. Synthesis and Anti-Chagas Activity Profile of a Redox-Active Lead 3-Benzylmenadione Revealed by High-Content Imaging. ACS Infect Dis 2024; 10:1808-1838. [PMID: 38606978 DOI: 10.1021/acsinfecdis.4c00137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Chagas disease, or American trypanosomiasis, is a neglected tropical disease which is a top priority target of the World Health Organization. The disease, endemic mainly in Latin America, is caused by the protozoan Trypanosoma cruzi and has spread around the globe due to human migration. There are multiple transmission routes, including vectorial, congenital, oral, and iatrogenic. Less than 1% of patients have access to treatment, relying on two old redox-active drugs that show poor pharmacokinetics and severe adverse effects. Hence, the priorities for the next steps of R&D include (i) the discovery of novel drugs/chemical classes, (ii) filling the pipeline with drug candidates that have new mechanisms of action, and (iii) the pressing need for more research and access to new chemical entities. In the present work, we first identified a hit (4a) with a potent anti-T. cruzi activity from a library of 3-benzylmenadiones. We then designed a synthetic strategy to build a library of 49 3-(4-monoamino)benzylmenadione derivatives via reductive amination to obtain diazacyclic benz(o)ylmenadiones. Among them, we identified by high content imaging an anti-amastigote "early lead" 11b (henceforth called cruzidione) revealing optimized pharmacokinetic properties and enhanced specificity. Studies in a yeast model revealed that a cruzidione metabolite, the 3-benzoylmenadione (cruzidione oxide), enters redox cycling with the NADH-dehydrogenase, generating reactive oxygen species, as hypothesized for the early hit (4a).
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Affiliation(s)
- Nathan Trometer
- UMR7042 CNRS-Unistra-UHA, Laboratoire d'Innovation Moléculaire et Applications (LIMA), Bio(in)organic & Medicinal Chemistry Team, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, F-67087 Strasbourg, France
| | - Jérémy Pecourneau
- UMR7042 CNRS-Unistra-UHA, Laboratoire d'Innovation Moléculaire et Applications (LIMA), Bio(in)organic & Medicinal Chemistry Team, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, F-67087 Strasbourg, France
| | - Liwen Feng
- UMR7042 CNRS-Unistra-UHA, Laboratoire d'Innovation Moléculaire et Applications (LIMA), Bio(in)organic & Medicinal Chemistry Team, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, F-67087 Strasbourg, France
| | - José A Navarro-Huerta
- UMR7042 CNRS-Unistra-UHA, Laboratoire d'Innovation Moléculaire et Applications (LIMA), Bio(in)organic & Medicinal Chemistry Team, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, F-67087 Strasbourg, France
| | - Danielle Lazarin-Bidóia
- Laboratório de Inovação Tecnológica no Desenvolvimento de Fármacos e Cosméticos, Departamento de Ciências Básicas da Saúde, Universidade Estadual de Maringá, CEP 87020-900 Paraná, Brazil
| | - Sueli de Oliveira Silva Lautenschlager
- Laboratório de Inovação Tecnológica no Desenvolvimento de Fármacos e Cosméticos, Departamento de Ciências Básicas da Saúde, Universidade Estadual de Maringá, CEP 87020-900 Paraná, Brazil
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, CDE-S7.27 Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Amanda Fortes Francisco
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - John M Kelly
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91198 Gif-sur-Yvette cedex, France
| | - Monica Cal
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, Petersgraben 1, CH-4001 Basel, Switzerland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, Petersgraben 1, CH-4001 Basel, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, Petersgraben 1, CH-4001 Basel, Switzerland
| | - Elisabeth Davioud-Charvet
- UMR7042 CNRS-Unistra-UHA, Laboratoire d'Innovation Moléculaire et Applications (LIMA), Bio(in)organic & Medicinal Chemistry Team, European School of Chemistry, Polymers and Materials (ECPM), 25, rue Becquerel, F-67087 Strasbourg, France
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3
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Sun Y, Zheng H, Qian L, Liu Y, Zhu D, Xu Z, Chang W, Xu J, Wang L, Sun B, Gu L, Yuan H, Lou H. Targeting GDP-Dissociation Inhibitor Beta (GDI2) with a Benzo[ a]quinolizidine Library to Induce Paraptosis for Cancer Therapy. JACS AU 2023; 3:2749-2762. [PMID: 37885576 PMCID: PMC10598831 DOI: 10.1021/jacsau.3c00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Inducing paraptosis, a nonapoptotic form of cell death, has great therapeutic potential in cancer therapy, especially for drug-resistant tumors. However, the specific molecular target(s) that trigger paraptosis have not yet been deciphered yet. Herein, by using activity-based protein profiling, we identified the GDP-dissociation inhibitor beta (GDI2) as a manipulable target for inducing paraptosis and uncovered benzo[a]quinolizidine BQZ-485 as a potent inhibitor of GDI2 through the interaction with Tyr245. Comprehensive target validation revealed that BQZ-485 disrupts the intrinsic GDI2-Rab1A interaction, thereby abolishing vesicular transport from the endoplasmic reticulum (ER) to the Golgi apparatus and initiating subsequent paraptosis events including ER dilation and fusion, ER stress, the unfolded protein response, and cytoplasmic vacuolization. Based on the structure of BQZ-485, we created a small benzo[a]quinolizidine library by click chemistry and discovered more potent GDI2 inhibitors using a NanoLuc-based screening platform. Leveraging the engagement of BQZ-485 with GDI2, we developed a selective GDI2 degrader. The optimized inhibitor (+)-37 and degrader 21 described in this study exhibited excellent in vivo antitumor activity in two GDI2-overexpressing pancreatic xenograft models, including an AsPc-1 solid tumor model and a transplanted human PDAC tumor model. Altogether, our findings provide a promising strategy for targeting GDI2 for paraptosis in the treatment of pancreatic cancers, and these lead compounds could be further optimized to be effective chemotherapeutics.
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Affiliation(s)
- Yong Sun
- Department
of Natural Products Chemistry, Key Laboratory of Natural Products
& Chemical Biology, Ministry of Education, School of Pharmaceutical
Sciences, Shandong University, Jinan 250012, China
| | - Hongbo Zheng
- Department
of Natural Products Chemistry, Key Laboratory of Natural Products
& Chemical Biology, Ministry of Education, School of Pharmaceutical
Sciences, Shandong University, Jinan 250012, China
| | - Lilin Qian
- Department
of Natural Products Chemistry, Key Laboratory of Natural Products
& Chemical Biology, Ministry of Education, School of Pharmaceutical
Sciences, Shandong University, Jinan 250012, China
| | - Yue Liu
- Department
of Natural Products Chemistry, Key Laboratory of Natural Products
& Chemical Biology, Ministry of Education, School of Pharmaceutical
Sciences, Shandong University, Jinan 250012, China
| | - Deyu Zhu
- Department
of Biochemistry and Molecular Biology, School of Basic Medical Sciences,
Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zejun Xu
- Department
of Natural Products Chemistry, Key Laboratory of Natural Products
& Chemical Biology, Ministry of Education, School of Pharmaceutical
Sciences, Shandong University, Jinan 250012, China
| | - Wenqiang Chang
- Department
of Natural Products Chemistry, Key Laboratory of Natural Products
& Chemical Biology, Ministry of Education, School of Pharmaceutical
Sciences, Shandong University, Jinan 250012, China
| | - Jianwei Xu
- Department
of General Surgery, Qilu Hospital of Shandong
University, Jinan 250012, China
| | - Lei Wang
- Department
of General Surgery, Qilu Hospital of Shandong
University, Jinan 250012, China
| | - Bin Sun
- National
Glycoengineering Research Center, Shandong
University, Jinan 250100, China
| | - Lichuan Gu
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Huiqing Yuan
- Key
Laboratory
of Experimental Teratology of the Ministry of Education, Institute
of Medical Sciences, The Second Hospital
of Shandong University, Jinan 250013, China
| | - Hongxiang Lou
- Department
of Natural Products Chemistry, Key Laboratory of Natural Products
& Chemical Biology, Ministry of Education, School of Pharmaceutical
Sciences, Shandong University, Jinan 250012, China
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4
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Krammer L, Breinbauer R. Activity‐Based Protein Profiling of Oxidases and Reductases. Isr J Chem 2023. [DOI: 10.1002/ijch.202200086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Leo Krammer
- Institute of Organic Chemistry Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
| | - Rolf Breinbauer
- Institute of Organic Chemistry Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
- BIOTECHMED Graz A-8010 Graz Austria
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5
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Carvalho L, Bernardes GJL. The Impact of Activity-based Protein Profiling in Malaria Drug Discovery. ChemMedChem 2022; 17:e202200174. [PMID: 35506504 PMCID: PMC9401580 DOI: 10.1002/cmdc.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/02/2022] [Indexed: 11/09/2022]
Abstract
Activity-based protein profiling (ABPP) is an approach used at the interface of chemical biology and proteomics that uses small molecular probes to provide dynamic fingerprints of enzymatic activity in complex proteomes. Malaria is a disease caused by Plasmodium parasites with a significant death burden and for which new therapies are actively being sought. Here, we compile the main achievements from ABPP studies in malaria and highlight the probes used and the different downstream platforms for data analysis. ABPP has excelled at studying Plasmodium cysteine proteases and serine hydrolase families, the targeting of the proteasome and metabolic pathways, and in the deconvolution of targets and mechanisms of known antimalarials. Despite the major impact in the field, many antimalarials and enzymatic families in Plasmodium remain to be studied, which suggests ABPP will be an evergreen technique in the field.
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Affiliation(s)
- Luis Carvalho
- University of Cambridge, Yusuf Hamied Department of Chemistry, Lensfield Rd, Yusuf Hamied Department of Chemistry, CB2 1EW, Cambridge, UNITED KINGDOM
| | - Gonçalo J L Bernardes
- University of Cambridge Department of Chemistry, Yusuf Hamied Department of Chemistry, Lensfield Rd, Yusuf Hamied Department of Chemistry, CB2 1EW, Cambridge, UNITED KINGDOM
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6
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de Rosa M, Nonnis S, Aliverti A. Covalent inhibition of P. falciparum ferredoxin-NADP + reductase: Exploring alternative strategies for the development of new antimalarial drugs. Biochem Biophys Res Commun 2021; 577:89-94. [PMID: 34509083 DOI: 10.1016/j.bbrc.2021.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/20/2022]
Abstract
The protozoan Plasmodium falciparum is the main aetiological agent of tropical malaria. Characteristic of the phylum is the presence of a plastid-like organelle which hosts several homologs of plant proteins, including a ferredoxin (PfFd) and its NADPH-dependent reductase (PfFNR). The PfFNR/PfFd redox system is essential for the parasite, while mammals share no homologous proteins, making the enzyme an attractive target for novel and much needed antimalarial drugs. Based on previous findings, three chemically reactive residues important for PfFNR activity were identified: namely, the active-site Cys99, responsible for hydride transfer; Cys284, whose oxidation leads to an inactive dimeric form of the protein; and His286, which is involved in NADPH binding. These amino acid residues were probed by several residue-specific reagents and the two cysteines were shown to be promising targets for covalent inhibition. The quantitative and qualitative description of the reactivity of few compounds, including a repurposed drug, set the bases for the development of more potent and specific antimalarial leads.
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Affiliation(s)
- Matteo de Rosa
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy.
| | - Simona Nonnis
- DIMEVET - Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy; CRC "Innovation for Well-Beeing and Environment" (I-WE), Università degli Studi di Milano, Milano, Italy
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