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Esposito S, Krick A, Pasquier O, Bonche F, Ingenito R, Magotti P, Bianchi E, Monteagudo E, Gallo M, Cicero DO, Orsatti L, Veneziano M, Caretti F, Mele R, Roversi D, Gennari N, Brasseur D, Gauzy-Lazo L, Duclos O, Mauriac C, Illiano S, Mallart S. Fatty acid acylated peptide therapeutics: discovery of omega-n oxidation of the lipid chain as a novel metabolic pathway in preclinical species. J Pharm Biomed Anal 2023; 227:115256. [PMID: 36764268 DOI: 10.1016/j.jpba.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023]
Abstract
We recently described C18 fatty acid acylated peptides as a new class of potent long-lasting single-chain RXFP1 agonists that displayed relaxin-like activities in vivo. Early pharmacokinetics and toxicological studies of these stearic acid acylated peptides revealed a relevant oxidative metabolism occurring in dog and minipig, and also seen at a lower extent in monkey and rat. Mass spectrometry combined to NMR spectroscopy studies revealed that the oxidation occurred, unexpectedly, on the stearic acid chain at ω-1, ω-2 and ω-3 positions. Structure-metabolism relationship studies on acylated analogues with different fatty acids lengths (C15-C20) showed that the extent of oxidation was higher with longer chains. The oxidized metabolites could be generated in vitro using liver microsomes and engineered bacterial CYPs. These systems were correlating poorly with in vivo metabolism observed across species; however, the results suggest that this biotransformation pathway might be catalyzed by some unknown CYP enzymes.
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Affiliation(s)
- Simone Esposito
- Biodistribution, Biotransformation and Analytical Science Unit, Experimental Pharmacology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy.
| | - Alain Krick
- DMPK France, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France.
| | - Olivier Pasquier
- DMPK France, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France
| | - Fabrice Bonche
- DMPK France, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France
| | - Raffaele Ingenito
- Peptide Chemistry Unit, Peptides & Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Paola Magotti
- Peptide Chemistry Unit, Peptides & Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Elisabetta Bianchi
- Peptide Chemistry Unit, Peptides & Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Edith Monteagudo
- Biodistribution, Biotransformation and Analytical Science Unit, Experimental Pharmacology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy; PK/PD & Bioanalytics Unit, Experimental Pharmacology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Mariana Gallo
- Structural Biology Unit, Computational Chemistry & Structural Biology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Daniel Oscar Cicero
- Department of Chemical Science and Technology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Laura Orsatti
- PK/PD & Bioanalytics Unit, Experimental Pharmacology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Maria Veneziano
- PK/PD & Bioanalytics Unit, Experimental Pharmacology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Fulvia Caretti
- PK/PD & Bioanalytics Unit, Experimental Pharmacology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Riccardo Mele
- Biodistribution, Biotransformation and Analytical Science Unit, Experimental Pharmacology Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Daniela Roversi
- Peptide Chemistry Unit, Peptides & Small Molecules R&D Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Nadia Gennari
- High Throughput Biology & Screening, Translational Research Department, IRBM Spa, Via Pontina Km 30 600, 00 071 Pomezia, Rome, Italy
| | - Denis Brasseur
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France
| | - Laurence Gauzy-Lazo
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France
| | - Olivier Duclos
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France
| | - Christine Mauriac
- DMPK France, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France
| | - Stephane Illiano
- Investigative Toxicology, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France
| | - Sergio Mallart
- Integrated Drug Discovery, Sanofi R&D, 1 rue Pierre Brossolette, 91385 Chilly Mazarin, France.
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Ciammaichella A, Ferrigno F, Basta A, D'Amico M, Biancofiore I, Nardi V, Ponzi S, Graziani R, Gennari N, Vittoria Orsale M, Fini I, Paonessa G, Summa V, Harper S, Ontoria JM. Optimization of 2-(1H-imidazo-2-yl)piperazines series of Trypanosoma brucei growth inhibitors as potential treatment for the second stage of HAT. Bioorg Med Chem Lett 2020; 30:127207. [PMID: 32354566 DOI: 10.1016/j.bmcl.2020.127207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 11/30/2022]
Abstract
A previous publication from our laboratory reported the identification of a new class of 2-(1H-imidazo-2-yl)piperazines as potent T. brucei growth inhibitors as potential treatment for Human African Trypanosomiasis (HAT). This work describes the structure-activity relationship (SAR) around the hit compound 1, which led to the identification of the optimized compound 18, a single digit nanomolar inhibitor (EC50 7 nM), not cytotoxic and with optimal in vivo profile that made it a suitable candidate for efficacy studies in a mouse model mimicking the second stage of disease.
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Affiliation(s)
- Alina Ciammaichella
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy.
| | - Federica Ferrigno
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Andreina Basta
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Melania D'Amico
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Ilaria Biancofiore
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Valentina Nardi
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Simona Ponzi
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Rita Graziani
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Nadia Gennari
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Maria Vittoria Orsale
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Ivan Fini
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Giacomo Paonessa
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Vincenzo Summa
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Steven Harper
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Jesus M Ontoria
- Departments of Chemistry and Biology, IRBM S.p.A, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
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Malancona S, Mori M, Fezzardi P, Santoriello M, Basta A, Nibbio M, Kovalenko L, Speziale R, Battista MR, Cellucci A, Gennari N, Monteagudo E, Di Marco A, Giannini A, Sharma R, Pires M, Real E, Zazzi M, Dasso Lang MC, De Forni D, Saladini F, Mely Y, Summa V, Harper S, Botta M. 5,6-Dihydroxypyrimidine Scaffold to Target HIV-1 Nucleocapsid Protein. ACS Med Chem Lett 2020; 11:766-772. [PMID: 32435383 DOI: 10.1021/acsmedchemlett.9b00608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/19/2020] [Indexed: 01/27/2023] Open
Abstract
The HIV-1 nucleocapsid (NC) protein is a small basic DNA and RNA binding protein that is absolutely necessary for viral replication and thus represents a target of great interest to develop new anti-HIV agents. Moreover, the highly conserved sequence offers the opportunity to escape the drug resistance (DR) that emerged following the highly active antiretroviral therapy (HAART) treatment. On the basis of our previous research, nordihydroguaiaretic acid 1 acts as a NC inhibitor showing moderate antiviral activity and suboptimal drug-like properties due to the presence of the catechol moieties. A bioisosteric catechol replacement approach led us to identify the 5-dihydroxypyrimidine-6-carboxamide substructure as a privileged scaffold of a new class of HIV-1 NC inhibitors. Hit validation efforts led to the identification of optimized analogs, as represented by compound 28, showing improved NC inhibition and antiviral activity as well as good ADME and PK properties.
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Affiliation(s)
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Paola Fezzardi
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | | | - Andreina Basta
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Martina Nibbio
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Lesia Kovalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | | | | | | | - Nadia Gennari
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | | | | | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Manuel Pires
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Eleonore Real
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Maria Chiara Dasso Lang
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | | | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci, 16, 50100 Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Vincenzo Summa
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Steven Harper
- IRBM S.p.A., Via Pontina Km 30.600, 00071 Pomezia, Rome, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
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Buonocore F, Picchietti S, Porcelli F, Della Pelle G, Olivieri C, Poerio E, Bugli F, Menchinelli G, Sanguinetti M, Bresciani A, Gennari N, Taddei AR, Fausto AM, Scapigliati G. Fish-derived antimicrobial peptides: Activity of a chionodracine mutant against bacterial models and human bacterial pathogens. Dev Comp Immunol 2019; 96:9-17. [PMID: 30790604 DOI: 10.1016/j.dci.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/07/2019] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
The increasing resistance to conventional antibiotics is an urgent problem that can be addressed by the discovery of new antimicrobial drugs such as antimicrobial peptides (AMPs). AMPs are components of innate immune system of eukaryotes and are not prone to the conventional mechanisms that are responsible of drug resistance. Fish are an important source of AMPs and, recently, we have isolated and characterized a new 22 amino acid residues peptide, the chionodracine (Cnd), from the Antarctic icefish Chionodraco hamatus. In this paper we focused on a new Cnd-derived mutant peptide, namely Cnd-m3a, designed to improve the selectivity against prokaryotic cells and the antimicrobial activity against human pathogens of the initial Cnd template. Cnd-m3a was used for immunization of rabbits, which gave rise to a polyclonal antibody able to detect the peptide. The interaction kinetic of Cnd-m3a with the Antarctic bacterium Psychrobacter sp. (TAD1) was imaged using a transmission electron microscopy (TEM) immunogold method. Initially the peptide was associated with the plasma membrane, but after 180 min of incubation, it was found in the cytoplasm interacting with a DNA target inside the bacterial cells. Using fluorescent probes we showed that the newly designed mutant can create pores in the outer membrane of the bacteria E. coli and Psychrobacter sp. (TAD1), confirming the results of TEM analysis. Moreover, in vitro assays demonstrated that Cnd-m3a is able to bind lipid vesicles of different compositions with a preference toward negatively charged ones, which mimics the prokaryotic cell. The Cnd-m3a peptide showed quite low hemolytic activity and weak cytotoxic effect against human primary and tumor cell lines, but high antimicrobial activity against selected Gram - human pathogens. These results highlighted the high potential of the Cnd-m3a peptide as a starting point for developing a new human therapeutic agent.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
| | - Simona Picchietti
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
| | - Fernando Porcelli
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
| | - Giulia Della Pelle
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
| | - Cristina Olivieri
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, 55455, USA.
| | - Elia Poerio
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
| | - Francesca Bugli
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy; Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Giulia Menchinelli
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy; Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Maurizio Sanguinetti
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy; Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.
| | | | - Nadia Gennari
- IRBM Science Park SpA, Biology Department, Rome, Italy.
| | - Anna Rita Taddei
- Center of Large Equipments, Section of Electron Microscopy, University of Tuscia, Viterbo, Italy.
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy.
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Guidi A, Saccoccia F, Gennari N, Gimmelli R, Nizi E, Lalli C, Paonessa G, Papoff G, Bresciani A, Ruberti G. Identification of novel multi-stage histone deacetylase (HDAC) inhibitors that impair Schistosoma mansoni viability and egg production. Parasit Vectors 2018; 11:668. [PMID: 30587243 PMCID: PMC6307185 DOI: 10.1186/s13071-018-3268-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022] Open
Abstract
Background Novel anti-schistosomal multi-stage drugs are needed because only a single drug, praziquantel, is available for the treatment of schistosomiasis and is poorly effective on larval and juvenile stages of the parasite. Schistosomes have a complex life-cycle and multiple developmental stages in the intermediate and definitive hosts. Acetylation and deacetylation of histones play pivotal roles in chromatin structure and in the regulation of transcription in eukaryotic cells. Histone deacetylase (HDAC) inhibitors modulate acetylation of several other proteins localized both in the nucleus and in the cytoplasm and therefore impact on many signaling networks and biological processes. Histone post-translational modifications may provide parasites with the ability to readily adapt to changes in gene expression required for their development and adaptation to the host environment. The aim of the present study was to screen a HDAC class I inhibitor library in order to identify and characterize novel multi-stage hit compounds. Methods We used a high-throughput assay based on the quantitation of ATP in the Schistosoma mansoni larval stage (schistosomula) and screened a library of 1500 class I HDAC inhibitors. Subsequently, a few hits were selected and further characterized by viability assays and phenotypic analyses on adult parasites by carmine red and confocal microscopy. Results Three compounds (SmI-124, SmI-148 and SmI-558) that had an effect on the viability of both the schistosomula larval stage and the adult worm were identified. Treatment with sub-lethal doses of SmI-148 and SmI-558 also decreased egg production. Moreover, treatment of adult parasites with SmI-148, and to a lesser extent Sm-124, was associated with histone hyperacetylation. Finally, SmI-148 and SmI-558 treatments of worm pairs caused a phenotype characterized by defects in the parasite reproductive system, with peculiar features in the ovary. In addition, SmI-558 induced oocyte- and vitelline cell-engulfment and signs of degeneration in the uterus and/or oviduct. Conclusions We report the screening of a small HDAC inhibitor library and the identification of three novel compounds which impair viability of the S. mansoni larval stage and adult pairs. These compounds are useful tools for studying deacetylase activity during parasite development and for interfering with egg production. Characterization of their specificity for selected S. mansoni versus human HDAC could provide insights that can be used in optimization and compound design.
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Affiliation(s)
- Alessandra Guidi
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | - Fulvio Saccoccia
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | - Nadia Gennari
- Biology Department, IRBM Science Park SpA, Pomezia, Italy
| | - Roberto Gimmelli
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | - Emanuela Nizi
- Chemistry Department, IRBM Science Park SpA, Pomezia, Italy
| | - Cristiana Lalli
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | | | - Giuliana Papoff
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | | | - Giovina Ruberti
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy.
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Nizi E, Sferrazza A, Fabbrini D, Nardi V, Andreini M, Graziani R, Gennari N, Bresciani A, Paonessa G, Harper S. Peptidomimetic nitrile inhibitors of malarial protease falcipain-2 with high selectivity against human cathepsins. Bioorg Med Chem Lett 2018; 28:1540-1544. [PMID: 29615344 DOI: 10.1016/j.bmcl.2018.03.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/19/2018] [Accepted: 03/24/2018] [Indexed: 10/17/2022]
Abstract
Falcipain-2 (FP2) is an essential enzyme in the lifecycle of malaria parasites such as Plasmodium falciparum, and its inhibition is viewed as an attractive mechanism of action for new anti-malarial agents. Selective inhibition of FP2 with respect to a family of human cysteine proteases (that include cathepsins B, K, L and S) is likely to be required for the development of agents targeting FP2. Here we describe a series of P2-modified aminonitrile based inhibitors of FP2 that provide a clear strategy toward addressing selectivity for the P. falciparum and show that it can provide potent FP2 inhibitors with strong selectivity against all four of these human cathepsin isoforms.
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Affiliation(s)
- Emanuela Nizi
- Department of Chemistry, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy.
| | - Alessio Sferrazza
- Department of Chemistry, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Danilo Fabbrini
- Department of Chemistry, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Valentina Nardi
- Department of Chemistry, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Matteo Andreini
- Department of Chemistry, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Rita Graziani
- Department of Biology, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Nadia Gennari
- Department of Biology, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Alberto Bresciani
- Department of Biology, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Giacomo Paonessa
- Department of Biology, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
| | - Steven Harper
- Department of Chemistry, IRBM Science Park, Via Pontina km 30, 600, Pomezia 00071, Rome, Italy
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7
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Guidi A, Lalli C, Gimmelli R, Nizi E, Andreini M, Gennari N, Saccoccia F, Harper S, Bresciani A, Ruberti G. Discovery by organism based high-throughput screening of new multi-stage compounds affecting Schistosoma mansoni viability, egg formation and production. PLoS Negl Trop Dis 2017; 11:e0005994. [PMID: 28985236 PMCID: PMC5646872 DOI: 10.1371/journal.pntd.0005994] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/18/2017] [Accepted: 09/26/2017] [Indexed: 11/22/2022] Open
Abstract
Schistosomiasis, one of the most prevalent neglected parasitic diseases affecting humans and animals, is caused by the Platyhelminthes of the genus Schistosoma. Schistosomes are the only trematodes to have evolved sexual dimorphism and the constant pairing with a male is essential for the sexual maturation of the female. Pairing is required for the full development of the two major female organs, ovary and vitellarium that are involved in the production of different cell types such as oocytes and vitellocytes, which represent the core elements of the whole egg machinery. Sexually mature females can produce a large number of eggs each day. Due to the importance of egg production for both life cycle and pathogenesis, there is significant interest in the search for new strategies and compounds not only affecting parasite viability but also egg production. Here we use a recently developed high-throughput organism-based approach, based on ATP quantitation in the schistosomula larval stage of Schistosoma mansoni for the screening of a large compound library, and describe a pharmacophore-based drug selection approach and phenotypic analyses to identify novel multi-stage schistosomicidal compounds. Interestingly, worm pairs treated with seven of the eight compounds identified show a phenotype characterized by defects in eggshell assemblage within the ootype and egg formation with degenerated oocytes and vitelline cells engulfment in the uterus and/or oviduct. We describe promising new molecules that not only impair the schistosomula larval stage but also impact juvenile and adult worm viability and egg formation and production in vitro. Schistosomiasis is a neglected disease caused by parasitic flatworms called schistosomes. The disease affects hundreds of millions of people in developing countries in the poorest tropical and subtropical regions of the world and it represents a major public health and socio-economical problem in several countries. In humans, these blood flukes reside in the mesenteric and vesicle venules. They have a life span of many years and produce hundreds of eggs daily, which are able to pass through the gut lumen or the bladder to be finally excreted into the environment for maintaining the life cycle. Part of the eggs can be trapped in host tissues inducing immunologically mediated granulomatous inflammation and fibrosis leading eventually to severe sequelae such as hepatosplenomegaly and even death. Importantly, schistosome infections increase susceptibility to other parasitic, bacterial and viral diseases. To date, essentially a single drug, praziquantel, is available to treat this parasitic disease. Despite its high tolerability and efficacy against adult parasites it has an incomplete efficacy across all stages of the S. mansoni life cycle and it does not prevent reinfection. Moreover the potential risk of drug resistance is an increasing concern. In search of novel schistosomicidal molecules we screened a large compound collection using the schistosomula, larval stage of the parasite. We identified eight novel molecules able to impair viability of schistosomula, juvenile and adult worms and also egg formation and production, two important features required for both disease transmission and progression.
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Affiliation(s)
- Alessandra Guidi
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | - Cristiana Lalli
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | - Roberto Gimmelli
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | - Emanuela Nizi
- IRBM Science Park SpA Chemistry Department, Pomezia, Italy
| | | | - Nadia Gennari
- IRBM Science Park SpA, Biology Department, Pomezia, Italy
| | - Fulvio Saccoccia
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
| | - Steven Harper
- IRBM Science Park SpA Chemistry Department, Pomezia, Italy
| | | | - Giovina Ruberti
- National Research Council, Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, Monterotondo (Roma), Italy
- * E-mail:
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8
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Ontoria JM, Paonessa G, Ponzi S, Ferrigno F, Nizi E, Biancofiore I, Malancona S, Graziani R, Roberts D, Willis P, Bresciani A, Gennari N, Cecchetti O, Monteagudo E, Orsale MV, Veneziano M, Di Marco A, Cellucci A, Laufer R, Altamura S, Summa V, Harper S. Discovery of a Selective Series of Inhibitors of Plasmodium falciparum HDACs. ACS Med Chem Lett 2016; 7:454-9. [PMID: 27190592 DOI: 10.1021/acsmedchemlett.5b00468] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/05/2016] [Indexed: 11/28/2022] Open
Abstract
The identification of a new series of P. falciparum growth inhibitors is described. Starting from a series of known human class I HDAC inhibitors a SAR exploration based on growth inhibitory activity in parasite and human cells-based assays led to the identification of compounds with submicromolar inhibition of P. falciparum growth (EC50 < 500 nM) and good selectivity over the activity of human HDAC in cells (up to >50-fold). Inhibition of parasital HDACs as the mechanism of action of this new class of selective growth inhibitors is supported by hyperacetylation studies.
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Affiliation(s)
- Jesus M. Ontoria
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Giacomo Paonessa
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Simona Ponzi
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Federica Ferrigno
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Emanuela Nizi
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Ilaria Biancofiore
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Savina Malancona
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Rita Graziani
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - David Roberts
- Medicines
for Malaria Venture, ICC, Route de Pré-Bois 20, P.O.
Box 1826, 1215 Geneva, Switzerland
| | - Paul Willis
- Medicines
for Malaria Venture, ICC, Route de Pré-Bois 20, P.O.
Box 1826, 1215 Geneva, Switzerland
| | - Alberto Bresciani
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Nadia Gennari
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Ottavia Cecchetti
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Edith Monteagudo
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Maria V. Orsale
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Maria Veneziano
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Annalise Di Marco
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Antonella Cellucci
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Ralph Laufer
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Sergio Altamura
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Vincenzo Summa
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
| | - Steven Harper
- Departments
of Chemistry and Biology, IRBM Science Park, Via Pontina km 30,600, 00071 Pomezia, Rome, Italy
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9
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Lalli C, Guidi A, Gennari N, Altamura S, Bresciani A, Ruberti G. Development and validation of a luminescence-based, medium-throughput assay for drug screening in Schistosoma mansoni. PLoS Negl Trop Dis 2015; 9:e0003484. [PMID: 25635836 PMCID: PMC4312041 DOI: 10.1371/journal.pntd.0003484] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/16/2014] [Indexed: 01/21/2023] Open
Abstract
Background Schistosomiasis, one of the world’s greatest neglected tropical diseases, is responsible for over 280,000 human deaths per annum. Praziquantel, developed in the 1970s, has high efficacy, excellent tolerability, few and transient side effects, simple administration procedures and competitive cost and it is currently the only recommended drug for treatment of human schistosomiasis. The use of a single drug to treat a population of over 200 million infected people appears particularly alarming when considering the threat of drug resistance. Quantitative, objective and validated methods for the screening of compound collections are needed for the discovery of novel anti-schistosomal drugs. Methodology/Principal Findings The present work describes the development and validation of a luminescence-based, medium-throughput assay for the detection of schistosomula viability through quantitation of ATP, a good indicator of metabolically active cells in culture. This validated method is demonstrated to be fast, highly reliable, sensitive and automation-friendly. The optimized assay was used for the screening of a small compound library on S. mansoni schistosomula, showing that the proposed method is suitable for a medium-throughput semi-automated screening. Interestingly, the pilot screening identified hits previously reported to have some anti-parasitic activity, further supporting the validity of this assay for anthelminthic drug discovery. Conclusions The developed and validated schistosomula viability luminescence-based assay was shown to be successful and suitable for the identification of novel compounds potentially exploitable in future schistosomiasis therapies. Schistosomiasis, one of the world’s greatest human neglected tropical diseases, is caused by a parasitic flatworm trematode of the genus Schistosoma. Among human parasitic diseases, schistosomiasis ranks second behind malaria in terms of socio-economic and public health importance in tropical and subtropical areas. More than 200 million people are currently infected in 77 countries, 85% of whom live in sub-Saharian Africa. To date no vaccine is available against schistosomiasis. As chemotherapy relies on a single drug, praziquantel, many initiatives have been promoted aiming to search for novel anti-schistosomal drugs that can represent a valid alternative to the current treatment or could be used in case of emerging resistance. Quantitative, objective and validated methods for compound collections screening are needed for the discovery of novel anti-schistosomal drugs. Here, we report the development and validation of a medium-throughput, luminescence-based assay for assessing viability at the schistosomulum stage of the human parasite S. mansoni. Our methodology enables a simple, reproducible, highly sensitive and objective quantitation of parasite viability. It is also automation compatible and enables the screening of compound collections thus hopefully contributing to the discovery of novel therapeutic strategies against schistosomiasis.
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Affiliation(s)
- Cristiana Lalli
- Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, National Research Council, Monterotondo, Rome, Italy
| | - Alessandra Guidi
- Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, National Research Council, Monterotondo, Rome, Italy
| | - Nadia Gennari
- Department of Biology, IRBM Science Park xSpA, Pomezia, Rome, Italy
| | - Sergio Altamura
- Department of Biology, IRBM Science Park xSpA, Pomezia, Rome, Italy
| | - Alberto Bresciani
- Department of Biology, IRBM Science Park xSpA, Pomezia, Rome, Italy
- * E-mail: (AB); (GR)
| | - Giovina Ruberti
- Institute of Cell Biology and Neurobiology, Campus A. Buzzati-Traverso, National Research Council, Monterotondo, Rome, Italy
- * E-mail: (AB); (GR)
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10
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Ontoria JM, Rydberg EH, Di Marco S, Tomei L, Attenni B, Malancona S, Martin Hernando JI, Gennari N, Koch U, Narjes F, Rowley M, Summa V, Carroll SS, Olsen DB, De Francesco R, Altamura S, Migliaccio G, Carfì A. Identification and biological evaluation of a series of 1H-benzo[de]isoquinoline-1,3(2H)-diones as hepatitis C virus NS5B polymerase inhibitors. J Med Chem 2010; 52:5217-27. [PMID: 19877603 DOI: 10.1021/jm900517t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells and, as a consequence, is an attractive target for inhibition. Herein, we present 1H-benzo[de]isoquinoline-1,3(2H)-diones as a new series of selective inhibitors of HCV NS5B polymerase. The HTS hit 1 shows submicromolar potency in two different HCV replicons (1b and 2b) and displays no activity on other polymerases (HIV-RT, Polio-pol, GBV-b-pol). These inhibitors act during the pre-elongation phase by binding to NS5B non-nucleoside binding site Thumb Site II as demonstrated by crystal structure of compound 1 with the DeltaC55-1b and DeltaC21-2b enzymes and by mutagenesis studies. SAR in this new series reveals inhibitors, such as 20, with low micromolar activity in the HCV replicon and with good activity/toxicity window in cells.
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Affiliation(s)
- Jesus M Ontoria
- Istituto Di Ricerche Di Biologia Molecolare, P. Angeletti, S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, I-00040 Pomezia, Italy.
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11
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Martin Hernando J, Ontoria J, Malancona S, Attenni B, Fiore F, Bonelli F, Koch U, Di Marco S, Colarusso S, Ponzi S, Gennari N, Vignetti S, del Rosario Rico Ferreira M, Habermann J, Rowley M, Narjes F. Optimization of Thienopyrrole-Based Finger-Loop Inhibitors of the Hepatitis C Virus NS5B Polymerase. ChemMedChem 2009; 4:1695-713. [DOI: 10.1002/cmdc.200900184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Gardelli C, Attenni B, Donghi M, Meppen M, Pacini B, Harper S, Di Marco A, Fiore F, Giuliano C, Pucci V, Laufer R, Gennari N, Marcucci I, Leone JF, Olsen DB, MacCoss M, Rowley M, Narjes F. Phosphoramidate Prodrugs of 2′-C-Methylcytidine for Therapy of Hepatitis C Virus Infection. J Med Chem 2009; 52:5394-407. [DOI: 10.1021/jm900447q] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cristina Gardelli
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Barbara Attenni
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Monica Donghi
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Malte Meppen
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Barbara Pacini
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Steven Harper
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Annalise Di Marco
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Fabrizio Fiore
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Claudio Giuliano
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Vincenzo Pucci
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Ralph Laufer
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Nadia Gennari
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Isabella Marcucci
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Joseph F. Leone
- Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065
| | - David B. Olsen
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Malcolm MacCoss
- Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065
| | - Michael Rowley
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Frank Narjes
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
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13
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Stansfield I, Avolio S, Colarusso S, Gennari N, Narjes F, Pacini B, Ponzi S, Harper S. Active site inhibitors of HCV NS5B polymerase. The development and pharmacophore of 2-thienyl-5,6-dihydroxypyrimidine-4-carboxylic acid. Bioorg Med Chem Lett 2005; 14:5085-8. [PMID: 15380204 DOI: 10.1016/j.bmcl.2004.07.075] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Revised: 07/23/2004] [Accepted: 07/29/2004] [Indexed: 01/02/2023]
Abstract
5,6-Dihydroxypyrimidine-4-carboxylic acids are a promising series of hepatitis C virus (HCV) NS5B polymerase inhibitors that bind at the active site of the enzyme. Here we report a simple 2-thienyl substituted analogue that shows 10-fold improved activity over the original lead, and which allowed us to further delineate the key elements of the pharmacophore of this class of inhibitor. This work led to the identification of a trifluoromethyl acylsulfonamide group as a viable replacement for the C4 carboxylic acid in this series.
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Affiliation(s)
- Ian Stansfield
- Department of Medicinal Chemistry, IRBM/MRL Rome, Via Pontina Km 30,600, Pomezia, 00040 Rome, Italy
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14
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Tomei L, Altamura S, Bartholomew L, Biroccio A, Ceccacci A, Pacini L, Narjes F, Gennari N, Bisbocci M, Incitti I, Orsatti L, Harper S, Stansfield I, Rowley M, De Francesco R, Migliaccio G. Mechanism of action and antiviral activity of benzimidazole-based allosteric inhibitors of the hepatitis C virus RNA-dependent RNA polymerase. J Virol 2004; 77:13225-31. [PMID: 14645579 PMCID: PMC296079 DOI: 10.1128/jvi.77.24.13225-13231.2003] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RNA-dependent RNA polymerase of hepatitis C virus (HCV) is the catalytic subunit of the viral RNA amplification machinery and is an appealing target for the development of new therapeutic agents against HCV infection. Nonnucleoside inhibitors based on a benzimidazole scaffold have been recently reported. Compounds of this class are efficient inhibitors of HCV RNA replication in cell culture, thus providing attractive candidates for further development. Here we report the detailed analysis of the mechanism of action of selected benzimidazole inhibitors. Kinetic data and binding experiments indicated that these compounds act as allosteric inhibitors that block the activity of the polymerase prior to the elongation step. Escape mutations that confer resistance to these compounds map to proline 495, a residue located on the surface of the polymerase thumb domain and away from the active site. Substitution of this residue is sufficient to make the HCV enzyme and replicons resistant to the inhibitors. Interestingly, proline 495 lies in a recently identified noncatalytic GTP-binding site, thus validating it as a potential allosteric site that can be targeted by small-molecule inhibitors of HCV polymerase.
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Affiliation(s)
- Licia Tomei
- Istituto di Ricerche di Biologia Molecolare "P. Angeletti," 00040 Pomezia-Rome, Italy.
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15
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Cerretani M, Di Renzo L, Serafini S, Vitelli A, Gennari N, Bianchi E, Pessi A, Urbani A, Colloca S, De Francesco R, Steinkühler C, Altamura S. A high-throughput radiometric assay for hepatitis C virus NS3 protease. Anal Biochem 1999; 266:192-7. [PMID: 9888975 DOI: 10.1006/abio.1998.2948] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A novel radiometric in vitro assay for discovery of inhibitors of hepatitis C viral protease activity, suitable for high-throughput screening, was developed. The NS3 protein of hepatitis C virus (HCV) contains a serine protease, whose function is to process the majority of the nonstructural proteins of the viral polyprotein. The viral NS4A protein is a cofactor of NS3 protease activity in the cleavage of NS3-NS4A, NS4A-NS4B, NS4B-NS5A, and NS5A-NS5B junctions. To establish an in vitro assay system we used NS3 proteases from different HCV strains, purified from Escherichia coli and a synthetic radiolabeled peptide substrate that mimics the NS4A-NS4B junction. Upon incubation with the enzyme the substrate was separated from the radiolabeled cleavage product by addition of an ion exchange resin. The assay was performed in a microtiter plate format and offered the potential for assaying numerous samples using a laboratory robot. Taking advantage of these features, we used the assay to optimize reaction conditions by simultaneously varying different buffer components. We showed that physicochemical conditions affect NS3 protease activity in a strain-specific way. Furthermore, the sensitivity of the assay makes it suitable for detection and detailed mechanistic characterization of inhibitors with low-nanomolar affinities for the HCV serine protease.
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Affiliation(s)
- M Cerretani
- Istituto di Ricerche di Biologia Molecolare (IRBM) "P. Angeletti,", Pomezia, Rome, 00040, Italy
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