1
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Narjes F, Edfeldt F, Petersen J, Öster L, Hamblet C, Bird J, Bold P, Rae R, Bäck E, Stomilovic S, Zlatoidsky P, Svensson T, Hidestål L, Kunalingam L, Shamovsky I, De Maria L, Gordon E, Lewis RJ, Watcham S, van Rietschoten K, Mudd GE, Harrison H, Chen L, Skynner MJ. Discovery and Characterization of a Bicyclic Peptide (Bicycle) Binder to Thymic Stromal Lymphopoietin. J Med Chem 2024; 67:2220-2235. [PMID: 38284169 DOI: 10.1021/acs.jmedchem.3c02163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/30/2024]
Abstract
Thymic stromal lymphopoietin (TSLP) is an epithelial-derived pro-inflammatory cytokine involved in the development of asthma and other atopic diseases. We used Bicycle Therapeutics' proprietary phage display platform to identify bicyclic peptides (Bicycles) with high affinity for TSLP, a target that is difficult to drug with conventional small molecules due to the extended protein-protein interactions it forms with both receptors. The hit series was shown to bind to TSLP in a hotspot, that is also used by IL-7Rα. Guided by the first X-ray crystal structure of a small peptide binding to TSLP and the identification of key metabolites, we were able to improve the proteolytic stability of this series in lung S9 fractions without sacrificing binding affinity. This resulted in the potent Bicycle 46 with nanomolar affinity to TSLP (KD = 13 nM), low plasma clearance of 6.4 mL/min/kg, and an effective half-life of 46 min after intravenous dosing to rats.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sophie Watcham
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | | | - Gemma E Mudd
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | - Helen Harrison
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | - Liuhong Chen
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
| | - Michael J Skynner
- BicycleTx Limited, Portway Building, Granta Park, Cambridge CB21 6GS, U.K
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2
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Zhao H, Narjes F. Kinetic Modeling of PROTAC-Induced Protein Degradation. ChemMedChem 2023; 18:e202300530. [PMID: 37905604 DOI: 10.1002/cmdc.202300530] [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: 10/03/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/02/2023]
Abstract
Kinetics of the PROTAC-induced protein degradation were modelled using the equilibrium approximation, accounting for the protein recovery rate with a time lag. The simulated kinetic curves resemble what is experimentally observed, and the physical formulas of the half-maximal degradation concentration (DC50 ) were derived from them. The equations reveal that DC50 is proportional to the dissociation constant of the ternary complex (Kd ) and inversely proportional to the expression level of the E3 ligase and the effective ubiquitylation rate (kub ). The predicted relationships were rigorously confirmed by experimental evidences from a matched molecular pair analysis using a set of published PROTACs.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43183, Sweden
| | - Frank Narjes
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43183, Sweden
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3
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Iegre J, Krajcovicova S, Gunnarsson A, Wissler L, Käck H, Luchniak A, Tångefjord S, Narjes F, Spring DR. A cell-active cyclic peptide targeting the Nrf2/Keap1 protein-protein interaction. Chem Sci 2023; 14:10800-10805. [PMID: 37829032 PMCID: PMC10566475 DOI: 10.1039/d3sc04083f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
The disruption of the protein-protein interaction (PPI) between Nrf2 and Keap1 is an attractive strategy to counteract the oxidative stress that characterises a variety of severe diseases. Peptides represent a complementary approach to small molecules for the inhibition of this therapeutically important PPI. However, due to their polar nature and the negative net charge required for binding to Keap1, the peptides reported to date exhibit either mid-micromolar activity or are inactive in cells. Herein, we present a two-component peptide stapling strategy to rapidly access a variety of constrained and functionalised peptides that target the Nrf2/Keap1 PPI. The most promising peptide, P8-H containing a fatty acid tag, binds to Keap1 with nanomolar affinity and is effective at inducing transcription of ARE genes in a human lung epithelial cell line at sub-micromolar concentration. Furthermore, crystallography of the peptide in complex with Keap1 yielded a high resolution X-ray structure, adding to the toolbox of structures available to develop cell-permeable peptidomimetic inhibitors.
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Affiliation(s)
- Jessica Iegre
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
| | - Sona Krajcovicova
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
- Department of Organic Chemistry, Palacky University Olomouc Tr. 17. Listopadu 12 77900 Olomouc Czech Republic
| | - Anders Gunnarsson
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Lisa Wissler
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Helena Käck
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Anna Luchniak
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Stefan Tångefjord
- BioScience, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - Frank Narjes
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca Pepparedsleden 1 43183 Gothenburg Sweden
| | - David R Spring
- Yusuf Hamied Department of Chemistry Lensfield Road CB2 1EW Cambridge UK
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4
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Wesche F, De Maria L, Leek T, Narjes F, Bird J, Su W, Czechtizky W. Analyzing proteolytic stability and metabolic hotspots of therapeutic peptides in two rodent pulmonary fluids. J Pharm Biomed Anal 2023; 224:115156. [PMID: 36463768 DOI: 10.1016/j.jpba.2022.115156] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/20/2022]
Abstract
Peptides and peptide drug conjugates are emerging modalities to treat pulmonary diseases. Peptides are susceptible to proteolytic cleavage. Expression levels of specific proteases in the lung can be significantly increased in disease state and may lead to exaggerated peptide proteolysis. To support optimization of peptides for inhaled administration, we have recently reported a streamlined high-throughput LC-HRMS protocol to determine enzymatic protease stability of peptides. This method has now been complemented with profiling of peptide metabolic stability in two respiratory fluids, a lung supernatant (lung S9) and a bronchioalveolar lavage fluid (BALF) taken from rats. We have tested a set of 28 peptides with high structural diversity, analyzed the whole data set for formed metabolites, and identified the differences of cleavage pattern in the two test fluids. Comparison of our experimental results and literature-derived cleavage site estimates based on e.g. MEROPS show significant differences for a number of peptides. This indicates the need for an experimental workflow using both protease panels and testing of metabolic stability in lung fluid (BALF) to guide peptide optimization and selection of peptides for inhaled in vivo PK/PD studies in our drug discovery projects.
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Affiliation(s)
- Frank Wesche
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, 88400 Biberach an der Riss, Germany; Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tomas Leek
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Frank Narjes
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - James Bird
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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5
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Wesche F, De Maria L, Leek T, Narjes F, Bird J, Su W, Czechtizky W. Automated high-throughput in vitro assays to identify metabolic hotspots and protease stability of structurally diverse, pharmacologically active peptides for inhalation. J Pharm Biomed Anal 2021; 211:114518. [DOI: 10.1016/j.jpba.2021.114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/27/2022]
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6
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Narjes F, Llinas A, von Berg S, Jirholt J, Lever S, Pehrson R, Collins M, Malmberg A, Svanberg P, Xue Y, Olsson RI, Malmberg J, Hughes G, Hossain N, Grindebacke H, Leffler A, Krutrök N, Bäck E, Ramnegård M, Lepistö M, Thunberg L, Aagaard A, McPheat J, Hansson EL, Chen R, Xiong Y, Hansson TG. AZD0284, a Potent, Selective, and Orally Bioavailable Inverse Agonist of Retinoic Acid Receptor-Related Orphan Receptor C2. J Med Chem 2021; 64:13807-13829. [PMID: 34464130 DOI: 10.1021/acs.jmedchem.1c01197] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 01/08/2023]
Abstract
Inverse agonists of the nuclear receptor RORC2 have been widely pursued as a potential treatment for a variety of autoimmune diseases. We have discovered a novel series of isoindoline-based inverse agonists of the nuclear receptor RORC2, derived from our recently disclosed RORC2 inverse agonist 2. Extensive structure-activity relationship (SAR) studies resulted in AZD0284 (20), which combined potent inhibition of IL-17A secretion from primary human TH17 cells with excellent metabolic stability and good PK in preclinical species. In two preclinical in vivo studies, compound 20 reduced thymocyte numbers in mice and showed dose-dependent reduction of IL-17A containing γδ-T cells and of IL-17A and IL-22 RNA in the imiquimod induced inflammation model. Based on these data and a favorable safety profile, 20 was progressed to phase 1 clinical studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yafeng Xue
- Mechanistic & Structural Biology, Discovery Science, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | | | | | | | | | | | | | | | | | | | | | - Linda Thunberg
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Anna Aagaard
- Mechanistic & Structural Biology, Discovery Science, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Jane McPheat
- Mechanistic & Structural Biology, Discovery Science, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Eva L Hansson
- Mechanistic & Structural Biology, Discovery Science, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Rongfeng Chen
- Pharmaron Beijing Co., Ltd., Taihe Road BDA, Beijing 100176, P. R. China
| | - Yao Xiong
- Pharmaron Beijing Co., Ltd., Taihe Road BDA, Beijing 100176, P. R. China
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7
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Shamovsky I, Ripa L, Narjes F, Bonn B, Schiesser S, Terstiege I, Tyrchan C. Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations. J Med Chem 2021; 64:8545-8563. [PMID: 34110134 DOI: 10.1021/acs.jmedchem.1c00514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aromatic and heteroaromatic amines (ArNH2) are activated by cytochrome P450 monooxygenases, primarily CYP1A2, into reactive N-arylhydroxylamines that can lead to covalent adducts with DNA nucleobases. Hereby, we give hands-on mechanism-based guidelines to design mutagenicity-free ArNH2. The mechanism of N-hydroxylation of ArNH2 by CYP1A2 is investigated by density functional theory (DFT) calculations. Two putative pathways are considered, the radicaloid route that goes via the classical ferryl-oxo oxidant and an alternative anionic pathway through Fenton-like oxidation by ferriheme-bound H2O2. Results suggest that bioactivation of ArNH2 follows the anionic pathway. We demonstrate that H-bonding and/or geometric fit of ArNH2 to CYP1A2 as well as feasibility of both proton abstraction by the ferriheme-peroxo base and heterolytic cleavage of arylhydroxylamines render molecules mutagenic. Mutagenicity of ArNH2 can be removed by structural alterations that disrupt geometric and/or electrostatic fit to CYP1A2, decrease the acidity of the NH2 group, destabilize arylnitrenium ions, or disrupt their pre-covalent transition states with guanine.
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8
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Valeur E, Narjes F, Ottmann C, Plowright AT. Emerging modes-of-action in drug discovery. Medchemcomm 2019; 10:1550-1568. [PMID: 31673315 PMCID: PMC6786009 DOI: 10.1039/c9md00263d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022]
Abstract
An increasing focus on complex biology to cure diseases rather than merely treat symptoms has transformed how drug discovery can be approached. Instead of activating or blocking protein function, a growing repertoire of drug modalities can be leveraged or engineered to hijack cellular processes, such as translational regulation or degradation mechanisms. Drug hunters can therefore access a wider arsenal of modes-of-action to modulate biological processes and this review summarises these emerging strategies by highlighting the most representative examples of these approaches.
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Affiliation(s)
- Eric Valeur
- Medicinal Chemistry , Research and Early Development, Cardiovascular, Renal & Metabolism , BioPharmaceuticals R&D , AstraZeneca, Gothenburg , 43183 Mölndal , Sweden .
| | - Frank Narjes
- Medicinal Chemistry , Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA) , BioPharmaceuticals R&D , AstraZeneca, Gothenburg , 43183 Mölndal , Sweden
| | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , Den Dolech 2 , 5612 , AZ , Eindhoven , the Netherlands
- Department of Chemistry , University of Duisburg-Essen , Universitätsstraße 7 , 45117 , Essen , Germany
| | - Alleyn T Plowright
- Integrated Drug Discovery , Sanofi-Aventis Deutschland GmbH , Industriepark Höchst , D-65926 Frankfurt am Main , Germany
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9
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von Berg S, Xue Y, Collins M, Llinas A, Olsson RI, Halvarsson T, Lindskog M, Malmberg J, Jirholt J, Krutrök N, Ramnegård M, Brännström M, Lundqvist A, Lepistö M, Aagaard A, McPheat J, Hansson EL, Chen R, Xiong Y, Hansson TG, Narjes F. Discovery of Potent and Orally Bioavailable Inverse Agonists of the Retinoic Acid Receptor-Related Orphan Receptor C2. ACS Med Chem Lett 2019; 10:972-977. [PMID: 31223457 DOI: 10.1021/acsmedchemlett.9b00158] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022] Open
Abstract
The further optimization of a recently disclosed series of inverse agonists of the nuclear receptor RORC2 is described. Investigations into the left-hand side of compound 1, guided by X-ray crystal structures, led to the substitution of the 4-aryl-thiophenyl residue with the hexafluoro-2-phenyl-propan-2-ol moiety. This change resulted in to compound 28, which combined improved drug-like properties with good cell potency and a significantly lower dose, using an early dose to man prediction. Target engagement in vivo was demonstrated in the thymus of mice by a reduction in the number of double positive T cells after oral dosing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rongfeng Chen
- Pharmaron Beijing Co., Ltd., Taihe Road BDA, Beijing 100176, P. R. China
| | - Yao Xiong
- Pharmaron Beijing Co., Ltd., Taihe Road BDA, Beijing 100176, P. R. China
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10
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Narjes F, Xue Y, von Berg S, Malmberg J, Llinas A, Olsson RI, Jirholt J, Grindebacke H, Leffler A, Hossain N, Lepistö M, Thunberg L, Leek H, Aagaard A, McPheat J, Hansson EL, Bäck E, Tångefjord S, Chen R, Xiong Y, Hongbin G, Hansson TG. Potent and Orally Bioavailable Inverse Agonists of RORγt Resulting from Structure-Based Design. J Med Chem 2018; 61:7796-7813. [DOI: 10.1021/acs.jmedchem.8b00783] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Linda Thunberg
- Early Product Development, Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, SE-43183 Mölndal, Sweden
| | - Hanna Leek
- Early Product Development, Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, SE-43183 Mölndal, Sweden
| | | | | | | | | | | | - Rongfeng Chen
- Pharmaron Beijing Company, Ltd., Taihe Road, BDA, Beijing 100176, PR China
| | - Yao Xiong
- Pharmaron Beijing Company, Ltd., Taihe Road, BDA, Beijing 100176, PR China
| | - Ge Hongbin
- Pharmaron Beijing Company, Ltd., Taihe Road, BDA, Beijing 100176, PR China
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11
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Shamovsky I, Belfield G, Lewis R, Narjes F, Ripa L, Tyrchan C, Öberg L, Sjö P. Theoretical studies of the second step of the nitric oxide synthase reaction: Electron tunneling prevents uncoupling. J Inorg Biochem 2018; 181:28-40. [PMID: 29407906 DOI: 10.1016/j.jinorgbio.2018.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 10/19/2017] [Revised: 12/18/2017] [Accepted: 01/08/2018] [Indexed: 12/27/2022]
Abstract
Nitric oxide (NO·) is a messenger molecule with diverse physiological roles including host defense, neurotransmission and vascular function. The synthesis of NO· from l-arginine is catalyzed by NO-synthases and occurs in two steps through the intermediary Nω-hydroxy-l-arginine (NHA). In both steps the P450-like reaction cycle is coupled with the redox cycle of the cofactor tetrahydrobiopterin (H4B). The mechanism of the second step is studied by Density Functional Theory calculations to ascertain the canonical sequence of proton and electron transfer (PT and ET) events. The proposed mechanism is controlled by the interplay of two electron donors, H4B and NHA. Consistent with experimental data, the catalytic cycle proceeds through the ferric-hydroperoxide complex (Cpd 0) and the following aqua-ferriheme resting state, and involves interim partial oxidation of H4B. The mechanism starts with formation of Cpd 0 from the ferrous-dioxy reactant complex by PT from the C-ring heme propionate coupled with hole transfer to H4B through the highest occupied π-orbital of NHA as a bridge. This enables PT from NHA+· to the proximal oxygen leading to the shallow ferriheme-H2O2 oxidant. Subsequent Fenton-like peroxide bond cleavage triggered by ET from the NHA-derived iminoxy-radical leads to the protonated Cpd II diradicaloid singlet stabilized by spin delocalization in H4B, and the closed-shell coordination complex of HO- with iminoxy-cation. The complex is converted to the transient C-adduct, which releases intended products upon PT to the ferriheme-HO- complex coupled with ET to the H4B+·. Deferred ET from the substrate or undue ET from/to the cofactor leads to side products.
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Affiliation(s)
- Igor Shamovsky
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden.
| | - Graham Belfield
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Richard Lewis
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Frank Narjes
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Lena Ripa
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Christian Tyrchan
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Lisa Öberg
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Peter Sjö
- Department of Medicinal Chemistry, IMED RIA, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83 Mölndal, Sweden
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12
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Olsson RI, Xue Y, von Berg S, Aagaard A, McPheat J, Hansson EL, Bernström J, Hansson P, Jirholt J, Grindebacke H, Leffler A, Chen R, Xiong Y, Ge H, Hansson TG, Narjes F. Back Cover: Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (T H17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor RORγ (ChemMedChem 2/2016). ChemMedChem 2016. [DOI: 10.1002/cmdc.201500605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Roine I. Olsson
- Department of Medicinal Chemistry; AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed; Pepparedsleden 1 43183 Mölndal Sweden
| | - Yafeng Xue
- Discovery Sciences; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Stefan von Berg
- Department of Medicinal Chemistry; AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed; Pepparedsleden 1 43183 Mölndal Sweden
| | - Anna Aagaard
- Discovery Sciences; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Jane McPheat
- Discovery Sciences; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Eva L. Hansson
- Discovery Sciences; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Jenny Bernström
- Discovery Sciences; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Pia Hansson
- Discovery Sciences; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Johan Jirholt
- Department of Bioscience; AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed; Pepparedsleden 1 43183 Mölndal Sweden
| | - Hanna Grindebacke
- Department of Bioscience; AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed; Pepparedsleden 1 43183 Mölndal Sweden
| | - Agnes Leffler
- Department of Bioscience; AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed; Pepparedsleden 1 43183 Mölndal Sweden
| | - Rongfeng Chen
- Department of Medicinal Chemistry; Pharmaron Beijing Co.; 6 Taihe Road, BDA Beijing 10076 P. R. China
| | - Yao Xiong
- Department of Medicinal Chemistry; Pharmaron Beijing Co.; 6 Taihe Road, BDA Beijing 10076 P. R. China
| | - Hongbin Ge
- Department of Medicinal Chemistry; Pharmaron Beijing Co.; 6 Taihe Road, BDA Beijing 10076 P. R. China
| | - Thomas G. Hansson
- Department of Medicinal Chemistry; AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed; Pepparedsleden 1 43183 Mölndal Sweden
| | - Frank Narjes
- Department of Medicinal Chemistry; AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed; Pepparedsleden 1 43183 Mölndal Sweden
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13
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Olsson RI, Xue Y, von Berg S, Aagaard A, McPheat J, Hansson EL, Bernström J, Hansson P, Jirholt J, Grindebacke H, Leffler A, Chen R, Xiong Y, Ge H, Hansson TG, Narjes F. Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (TH 17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor RORγ. ChemMedChem 2015; 11:207-16. [PMID: 26553345 DOI: 10.1002/cmdc.201500432] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [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: 09/21/2015] [Indexed: 12/20/2022]
Abstract
RORγt, an isoform of the retinoic acid-related orphan receptor gamma (RORc, RORγ), has been identified as the master regulator of T-helper 17 (TH 17) cell function and development, making it an attractive target for the treatment of autoimmune diseases. Validation for this target comes from antibodies targeting interleukin-17 (IL-17), the signature cytokine produced by TH 17 cells, which have shown impressive results in clinical trials. Through focused screening of our compound collection, we identified a series of N-sulfonylated benzoxazepines, which displayed micromolar affinity for the RORγ ligand-binding domain (LBD) in a radioligand binding assay. Optimization of these initial hits resulted in potent binders, which dose-dependently decreased the ability of the RORγ-LBD to interact with a peptide derived from steroid receptor coactivator 1, and inhibited the release of IL-17 secretion from isolated and cultured human TH 17 cells with nanomolar potency. A cocrystal structure of inverse agonist 15 (2-chloro-6-fluoro-N-(4-{[3-(trifluoromethyl)phenyl]sulfonyl}-2,3,4,5-tetrahydro-1,4-benzoxazepin-7-yl)benzamide) bound to the RORγ-LBD illustrated that both hydrophobic interactions, leading to an induced fit around the substituted benzamide moiety of 15, as well as a hydrogen bond from the amide NH to His479 seemed to be important for the mechanism of action. This structure is compared with the structure of agonist 25 (N-(2-fluorophenyl)-4-[(4-fluorophenyl)sulfonyl]-2,3,4,5-tetrahydro-1,4-benzoxazepin-6-amine ) and structures of other known RORγ modulators.
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Affiliation(s)
- Roine I Olsson
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Yafeng Xue
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Stefan von Berg
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Anna Aagaard
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Jane McPheat
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Eva L Hansson
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Jenny Bernström
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Pia Hansson
- Discovery Sciences, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Johan Jirholt
- Department of Bioscience, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Hanna Grindebacke
- Department of Bioscience, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Agnes Leffler
- Department of Bioscience, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Rongfeng Chen
- Department of Medicinal Chemistry, Pharmaron Beijing Co., 6 Taihe Road, BDA, Beijing, 10076, P. R. China
| | - Yao Xiong
- Department of Medicinal Chemistry, Pharmaron Beijing Co., 6 Taihe Road, BDA, Beijing, 10076, P. R. China
| | - Hongbin Ge
- Department of Medicinal Chemistry, Pharmaron Beijing Co., 6 Taihe Road, BDA, Beijing, 10076, P. R. China
| | - Thomas G Hansson
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - Frank Narjes
- Department of Medicinal Chemistry, AstraZeneca, Respiratory, Inflammation and Autoimmunity iMed, Pepparedsleden 1, 43183, Mölndal, Sweden.
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14
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Edfeldt F, Evenäs J, Lepistö M, Ward A, Petersen J, Wissler L, Rohman M, Sivars U, Svensson K, Perry M, Feierberg I, Zhou XH, Hansson T, Narjes F. Identification of indole inhibitors of human hematopoietic prostaglandin D2 synthase (hH-PGDS). Bioorg Med Chem Lett 2015; 25:2496-500. [DOI: 10.1016/j.bmcl.2015.04.065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/19/2015] [Accepted: 04/20/2015] [Indexed: 11/25/2022]
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15
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Colarusso S, Habermann J, Conte I, Di Filippo M, Ercolani C, Mackay A, Palumbi M, Rico Ferreira MDR, Stansfield I, Zaramella S, Narjes F. Development of a Scalable Chiral Synthesis of MK-3281, an Inhibitor of the Hepatitis C Virus NS5B Polymerase. Synlett 2011. [DOI: 10.1055/s-0030-1260790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Narjes F, Crescenzi B, Ferrara M, Habermann J, Colarusso S, Ferreira MDRR, Stansfield I, Mackay AC, Conte I, Ercolani C, Zaramella S, Palumbi MC, Meuleman P, Leroux-Roels G, Giuliano C, Fiore F, Di Marco S, Baiocco P, Koch U, Migliaccio G, Altamura S, Laufer R, De Francesco R, Rowley M. Discovery of (7R)-14-cyclohexyl-7-{[2-(dimethylamino)ethyl](methyl) amino}-7,8-dihydro-6H-indolo[1,2-e][1,5]benzoxazocine-11-carboxylic acid (MK-3281), a potent and orally bioavailable finger-loop inhibitor of the hepatitis C virus NS5B polymerase. J Med Chem 2010; 54:289-301. [PMID: 21141896 DOI: 10.1021/jm1013105] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral genome and has been a prime target for drug discovery efforts. Here, we report on the further development of tetracyclic indole inhibitors, binding to an allosteric site on the thumb domain. Structure-activity relationship (SAR) studies around an indolo-benzoxazocine scaffold led to the identification of compound 33 (MK-3281), an inhibitor with good potency in the HCV subgenomic replication assay and attractive molecular properties suitable for a clinical candidate. The compound caused a consistent decrease in viremia in vivo using the chimeric mouse model of HCV infection.
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Affiliation(s)
- Frank Narjes
- Istituto Di Ricerche Di Biologia Molecolare, P. Angeletti SpA (Merck Research Laboratories, Rome), Pomezia, Italy.
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17
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Cianetti S, Cooper VB, Attenni B, Pucci V, Fiore F, Giuliano C, Laufer R, Gardelli C, Monteagudo E, Narjes F, Pearce GE, Rowley M. Enhancement of intestinal absorption of 2-methyl cytidine prodrugs. Drug Deliv 2010; 17:214-22. [PMID: 20233089 DOI: 10.3109/10717541003667814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The purpose of this study was to investigate the in vivo absorption enhancement of a nucleoside (phosphoramidate prodrug of 2'-methyl-cytidine) anti-viral agent of proven efficacy by means of intestinal permeation enhancers. Natural nucleosides are hydrophilic molecules that do not rapidly penetrate cell membranes by diffusion and their absorption relies on specialized transporters. Therefore, the oral absorption of nucleoside prodrugs and the target organ concentration of the biologically active nucleotide can be limited due to poor permeation across the intestinal epithelium. In the present study, the specificity, concentration dependence, and effect of four classes of absorption promoters, i.e. fatty acids, steroidal detergents, mucoadhesive polymers, and secretory transport inhibitors, were evaluated in a rat in vivo model. Sodium caprate and alpha-tocopheryl-polyethyleneglycol-1000-succinate (TPGS) showed a significant effect in increasing liver concentration of nucleotide (5-fold). These results suggested that both excipients might be suited in a controlled release matrix for the synchronous release of the drug and absorption promoter directly to the site of absorption and highlights that the effect is strictly dependent on the absorption promoter dose. The feasibility of such a formulation approach in humans was evaluated with the aim of developing a solid dosage form for the peroral delivery of nucleosides and showed that these excipients do provide a potential valuable tool in pre-clinical efficacy studies to drive discovery programs forward.
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Affiliation(s)
- Simona Cianetti
- IRBM, Merck Research Laboratories, Via Pontina Km 30600, 00040, Pomezia (RM), Italy.
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18
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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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19
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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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20
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Meppen M, Pacini B, Bazzo R, Koch U, Leone JF, Koeplinger KA, Rowley M, Altamura S, Di Marco A, Fiore F, Giuliano C, Gonzalez-Paz O, Laufer R, Pucci V, Narjes F, Gardelli C. Cyclic phosphoramidates as prodrugs of 2′-C-methylcytidine. Eur J Med Chem 2009; 44:3765-70. [DOI: 10.1016/j.ejmech.2009.04.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 04/29/2009] [Accepted: 04/30/2009] [Indexed: 11/24/2022]
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21
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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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22
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Ponzi S, Habermann J, del Rosario Rico Ferreira M, Narjes F. Synthesis of Indolo[2,1-a][2]benzazepine
and Indolo[2,1-a][2]-benzazocine. Synlett 2009. [DOI: 10.1055/s-0029-1217168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Habermann J, Capitò E, Ferreira MDRR, Koch U, Narjes F. Discovery of pentacyclic compounds as potent inhibitors of hepatitis C virus NS5B RNA polymerase. Bioorg Med Chem Lett 2009; 19:633-8. [DOI: 10.1016/j.bmcl.2008.12.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 12/05/2008] [Accepted: 12/07/2008] [Indexed: 10/21/2022]
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24
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Conte I, Giuliano C, Ercolani C, Narjes F, Koch U, Rowley M, Altamura S, De Francesco R, Neddermann P, Migliaccio G, Stansfield I. Synthesis and SAR of piperazinyl-N-phenylbenzamides as inhibitors of hepatitis C virus RNA replication in cell culture. Bioorg Med Chem Lett 2009; 19:1779-83. [PMID: 19216075 DOI: 10.1016/j.bmcl.2009.01.066] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/20/2009] [Accepted: 01/22/2009] [Indexed: 12/17/2022]
Abstract
The RNA replication machinery of HCV is a multi-subunit membrane-associated complex. NS5A has emerged as an active component of HCV replicase, possibly involved in regulation of viral replication and resistance to the antiviral effect of interferon. We report here substituted piperazinyl-N-(aryl)benzamides as potent inhibitors of HCV replication exerted via modulation of the dimerization of NS5A.
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Affiliation(s)
- Immacolata Conte
- Department of Medicinal Chemistry, Istituto di Ricerche di Biologia Molecolare "P. Angeletti" S.p.A., Merck Research Laboratories Rome, 00040 Pomezia, Rome, Italy
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25
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Gallo M, Pennestri M, Bottomley MJ, Barbato G, Eliseo T, Paci M, Narjes F, De Francesco R, Summa V, Koch U, Bazzo R, Cicero DO. Binding of a Noncovalent Inhibitor Exploiting the S′ region Stabilizes the Hepatitis C virus NS3 Protease Conformation in the Absence of Cofactor. J Mol Biol 2009; 385:1142-55. [DOI: 10.1016/j.jmb.2008.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 10/17/2008] [Accepted: 11/12/2008] [Indexed: 12/09/2022]
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26
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Giuliano C, Fiore F, Di Marco A, Padron Velazquez J, Bishop A, Bonelli F, Gonzalez-Paz O, Marcucci I, Harper S, Narjes F, Pacini B, Monteagudo E, Migliaccio G, Rowley M, Laufer R. Preclinical pharmacokinetics and metabolism of a potent non-nucleoside inhibitor of the hepatitis C virus NS5B polymerase. Xenobiotica 2008; 35:1035-54. [PMID: 16393860 DOI: 10.1080/00498250500356548] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [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: 10/25/2022]
Abstract
The disposition of compound A, a potent inhibitor of the hepatitis C virus (HCV) NS5B polymerase, was characterized in animals in support of its selection for further development. Compound A exhibited marked species differences in pharmacokinetics. Plasma clearance was 44 ml min-1 kg-1 in rats, 9 ml min-1 kg-1 in dogs and 16 ml min-1 kg-1 in rhesus monkeys. Oral bioavailability was low in rats (10%) but significantly higher in dogs (52%) and monkeys (26%). Compound A was eliminated primarily by metabolism in rats, with biliary excretion accounting for 30% of its clearance. Metabolism was mainly mediated by cyclohexyl hydroxylation, with N-deethylation and acyl glucuronide formation constituting minor metabolic pathways. Qualitatively, the same metabolites were identified using in vitro systems from all species studied, including humans. The low oral bioavailability of compound A in rats was mostly due to poor intestinal absorption. This conclusion was borne out by the findings that hepatic extraction in the rat was only 30%, intraperitoneal bioavailability was good, and compound A was poorly absorbed from the rat isolated intestinal loop, with no detectable intestinal metabolism. Compound A was not an inhibitor of major human cytochrome P450 enzymes, indicating minimal potential for clinical drug-drug interactions. The metabolic clearance of compound A in rat, dog and monkey hepatocytes correlated with the systemic clearance observed in these species. Since compound A was very stable in human hepatocytes, the results suggest that it will be a low clearance drug in humans.
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Affiliation(s)
- C Giuliano
- Department of Pharmacology, Istituto di Ricerche di Biologia Molecolare (IRBM) P. Angeletti, Merck Research Laboratories Rome, Pomezia, Italy
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27
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Abstract
The global prevalence of hepatitis C virus (HCV) infection and the serious consequences associated with the chronic state of the disease have become a worldwide health problem. A combination therapy comprising Interferon-alpha and Ribavirin represents the current standard treatment for chronic HCV infection, although it has demonstrated limited success and causes serious side effects. Promising alternative approaches toward the control of HCV infection include the development of small molecule inhibitors of viral enzymes interfering with the essential steps in the life cycle of the virus. In this review we will focus on inhibitors of the HCV-encoded NS5B RNA-dependent RNA polymerase (NS5B RdRp) which is essential for viral replication and has been recognized as a prime target for therapeutic intervention.
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Affiliation(s)
- Uwe Koch
- Istituto di Ricerche di Biologia Molecolare P. Angeletti S.P.A.-Merck Research Laboratories, Rome, Italy
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28
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Stansfield I, Pompei M, Conte I, Ercolani C, Migliaccio G, Jairaj M, Giuliano C, Rowley M, Narjes F. Development of carboxylic acid replacements in indole-N-acetamide inhibitors of hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2007; 17:5143-9. [PMID: 17681757 DOI: 10.1016/j.bmcl.2007.06.093] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [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: 05/16/2007] [Revised: 06/28/2007] [Accepted: 06/29/2007] [Indexed: 12/16/2022]
Abstract
Allosteric inhibition of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase enzyme has recently emerged as a viable strategy toward blocking replication of viral RNA in cell-based systems. We report here 2 series of indole-N-acetamides, bearing physicochemically diverse carboxylic acid replacements, which show potent affinity for the NS5B enzyme with reduced potential for formation of glucuronide conjugates. Preliminary optimization of these series furnished compounds that are potent in the blockade of subgenomic HCV RNA replication in HUH-7 cells.
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Affiliation(s)
- Ian Stansfield
- IRBM (Merck Research Laboratories Rome), Via Pontina Km 30,600, 00040 Pomezia, Rome, Italy.
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29
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Ontoria JM, Martìn Hernando JI, Malancona S, Attenni B, Stansfield I, Conte I, Ercolani C, Habermann J, Ponzi S, Di Filippo M, Koch U, Rowley M, Narjes F. Identification of thieno[3,2-b]pyrroles as allosteric inhibitors of hepatitis C virus NS5B polymerase. Bioorg Med Chem Lett 2006; 16:4026-30. [PMID: 16714108 DOI: 10.1016/j.bmcl.2006.05.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [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: 02/09/2006] [Revised: 05/02/2006] [Accepted: 05/03/2006] [Indexed: 10/24/2022]
Abstract
Thieno[3,2-b]pyrroles are a novel class of allosteric inhibitors of HCV NS5B RNA-dependent RNA polymerase which show potent affinity for the NS5B enzyme. Introduction of a polar substituent in the position N1 led to a compound that efficiently blocks subgenomic HCV RNA replication in HUH-7 cells with an EC50 of 2.9 microM.
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Affiliation(s)
- Jesus M Ontoria
- Department of Medicinal Chemistry, IRBM-MRL Rome, Via Pontina, Km 30.600, 00040 Pomezia (Rome), Italy.
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30
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Abstract
The human and monetary costs of chronic hepatitis C and the complications arising from this disease emphasize the urgency to find a treatment for Hepatitis C Virus (HCV) infected patients. The current standard of treatment for patients chronically infected with HCV is combination therapy with pegylated interferon plus ribavirin. Recently, viral enzymes have become the target of efforts to develop small molecule inhibitors interfering with the essential steps in the life cycle of the virus. Amongst these enzymes the HCV-encoded NS5B RNA-dependent RNA polymerase (NS5B RdRp) is essential for viral replication and has been recognized as a prime target for therapeutic intervention. Several distinct classes of inhibitors of NS5B RdRp have been disclosed in the literature, including active site inhibitors such as nucleosides and pyrophosphate mimetics, as well as non-nucleoside inhibitors. The latter, based on the success of allosteric inhibitors in the treatment of HIV infection, have been developed into compounds which show activity in the subgenomic cell-culture assay of HCV replication. This review provides an account of the recent developments in this field.
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Affiliation(s)
- Uwe Koch
- Istituto di Ricerche di Biologia Molecolare P. Angeletti S.P.A. -- Merck Research Laboratories, Rome, Via Pontina km 30,600, 00040 Pomezia (Rome), Italy
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31
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Koch U, Attenni B, Malancona S, Colarusso S, Conte I, Di Filippo M, Harper S, Pacini B, Giomini C, Thomas S, Incitti I, Tomei L, De Francesco R, Altamura S, Matassa VG, Narjes F. 2-(2-Thienyl)-5,6-dihydroxy-4-carboxypyrimidines as inhibitors of the hepatitis C virus NS5B polymerase: discovery, SAR, modeling, and mutagenesis. J Med Chem 2006; 49:1693-705. [PMID: 16509585 DOI: 10.1021/jm051064t] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [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: 12/09/2022]
Abstract
Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral RNA. We recently disclosed dihydroxypyrimidine carboxylates 2 as novel, reversible inhibitors of the HCV NS5B polymerase. This series was further developed into 5,6-dihydroxy-2-(2-thienyl)pyrimidine-4-carboxylic acids such as 34 (EC50 9.3 microM), which now show activity in the cell-based HCV replication assay. The structure-activity relationship of these inhibitors is discussed in the context of their physicochemical properties and of the polymerase crystal structure. We also report the results of mutagenesis experiments which support the proposed binding model, which involves pyrophosphate-like chelation of the active site Mg ions.
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Affiliation(s)
- Uwe Koch
- Istituto Di Ricerche Di Biologia Molecolare, P. Angeletti S.p.A. (Merck Research Laboratories, Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy.
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32
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Colarusso S, Girardin M, Conte I, Narjes F. Suzuki Coupling at the 2-Position of Densely Functionalized Pyrimidones. SYNTHESIS-STUTTGART 2006. [DOI: 10.1055/s-2006-926414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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Attenni B, Avolio S, Colarusso S, Malancona S, Harper S, Altamura S, Koch U, Narjes F. Inhibitors of the hepatitis C virus RNA-dependent RNA polymerase. ARKIVOC 2006. [DOI: 10.3998/ark.5550190.0007.733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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34
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Di Marco S, Volpari C, Tomei L, Altamura S, Harper S, Narjes F, Koch U, Rowley M, De Francesco R, Migliaccio G, Carfí A. Interdomain communication in HCV polymerase abolished by small-molecule inhibitors. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305089531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Harper S, Avolio S, Pacini B, Di Filippo M, Altamura S, Tomei L, Paonessa G, Di Marco S, Carfi A, Giuliano C, Padron J, Bonelli F, Migliaccio G, De Francesco R, Laufer R, Rowley M, Narjes F. Potent Inhibitors of Subgenomic Hepatitis C Virus RNA Replication through Optimization of Indole-N-Acetamide Allosteric Inhibitors of the Viral NS5B Polymerase. J Med Chem 2005; 48:4547-57. [PMID: 15999993 DOI: 10.1021/jm050056+] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [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: 11/29/2022]
Abstract
Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. Compounds that block replication of subgenomic HCV RNA in liver cells are of interest because of their demonstrated antiviral effect in the clinic. In followup to our recent report that indole-N-acetamides (e.g., 1) are potent allosteric inhibitors of the HCV NS5B polymerase enzyme, we describe here their optimization as cell-based inhibitors. The crystal structure of 1 bound to NS5B was a guide in the design of a two-dimensional compound array that highlighted that formally zwitterionic inhibitors have strong intracellular potency and that pregnane X receptor (PXR) activation (an undesired off-target activity) is linked to a structural feature of the inhibitor. Optimized analogues devoid of PXR activation (e.g., 55, EC(50) = 127 nM) retain strong cell-based efficacy under high serum conditions and show acceptable pharmacokinetics parameters in rat and dog.
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Affiliation(s)
- Steven Harper
- IRBM (Merck Research Laboratories, Rome), Pomezia, Italy.
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36
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Di Marco S, Volpari C, Tomei L, Altamura S, Harper S, Narjes F, Koch U, Rowley M, De Francesco R, Migliaccio G, Carfí A. Interdomain communication in hepatitis C virus polymerase abolished by small molecule inhibitors bound to a novel allosteric site. J Biol Chem 2005; 280:29765-70. [PMID: 15955819 DOI: 10.1074/jbc.m505423200] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [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: 01/09/2023] Open
Abstract
The hepatitis C virus (HCV) polymerase is required for replication of the viral genome and is a key target for therapeutic intervention against HCV. We have determined the crystal structures of the HCV polymerase complexed with two indole-based allosteric inhibitors at 2.3- and 2.4-Angstroms resolution. The structures show that these inhibitors bind to a site on the surface of the thumb domain. A cyclohexyl and phenyl ring substituents, bridged by an indole moiety, fill two closely spaced pockets, whereas a carboxylate substituent forms a salt bridge with an exposed arginine side chain. Interestingly, in the apoenzyme, the inhibitor binding site is occupied by a small alpha-helix at the tip of the N-terminal loop that connects the fingers and thumb domains. Thus, these molecules inhibit the enzyme by preventing formation of intramolecular contacts between these two domains and consequently precluding their coordinated movements during RNA synthesis. Our structures identify a novel mechanism by which a new class of allosteric inhibitors inhibits the HCV polymerase and open the way to the development of novel antiviral agents against this clinically relevant human pathogen.
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Affiliation(s)
- Stefania Di Marco
- Istituto di Ricerche di Biologia Molecolare P. Angeletti, Pomezia (Rome), Italy
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37
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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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38
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Harper S, Pacini B, Avolio S, Di Filippo M, Migliaccio G, Laufer R, De Francesco R, Rowley M, Narjes F. Development and Preliminary Optimization of Indole-N-Acetamide Inhibitors of Hepatitis C Virus NS5B Polymerase. J Med Chem 2005; 48:1314-7. [PMID: 15743173 DOI: 10.1021/jm049122i] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [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: 11/30/2022]
Abstract
Allosteric inhibition of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase enzyme has recently emerged as a viable strategy toward blocking replication of viral RNA in cell-based systems. We report here a novel class of allosteric inhibitor of NS5B that shows potent affinity for the NS5B enzyme and effective inhibition of subgenomic HCV RNA replication in HUH-7 cells. Inhibitors from this class have promising characteristics for further development as anti-HCV agents.
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Affiliation(s)
- Steven Harper
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy.
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39
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Colarusso S, Gerlach B, Giuliano C, Koch U, Matassa V, Narjes F. The Role of an Amphiphilic Capping Group in Covalent and Non-Covalent Dipeptide Inhibitors of HCV NS3 Serine Protease. LETT DRUG DES DISCOV 2005. [DOI: 10.2174/1570180053175089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Malancona S, Colarusso S, Ontoria JM, Marchetti A, Poma M, Stansfield I, Laufer R, Di Marco A, Taliani M, Verdirame M, Gonzalez-Paz O, Matassa VG, Narjes F. SAR and pharmacokinetic studies on phenethylamide inhibitors of the hepatitis C virus NS3/NS4A serine protease. Bioorg Med Chem Lett 2005; 14:4575-9. [PMID: 15357995 DOI: 10.1016/j.bmcl.2004.05.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [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: 02/09/2004] [Revised: 05/21/2004] [Accepted: 05/27/2004] [Indexed: 12/22/2022]
Abstract
SAR on the phenethylamide 1 (Ki 1.2 microM) in the P2- and the P'-position led to potent inhibitors, one of which showed good exposure and low clearance when administered intramuscularly to rat.
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Affiliation(s)
- Savina Malancona
- Department of Chemistry, Istituto di Ricerche di Biologia Molecolare, Merck Research Laboratories, Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy
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41
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Nizi E, Koch U, Ontoria JM, Marchetti A, Narjes F, Malancona S, Matassa VG, Gardelli C. Capped dipeptide phenethylamide inhibitors of the HCV NS3 protease. Bioorg Med Chem Lett 2004; 14:2151-4. [PMID: 15080998 DOI: 10.1016/j.bmcl.2004.02.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [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: 10/28/2003] [Revised: 02/06/2004] [Accepted: 02/09/2004] [Indexed: 12/09/2022]
Abstract
The N-terminal aminoacid of phenethylamide tripeptide inhibitors of the hepatitis C virus NS3 protease can be replaced with an alpha-hydroxy acid to obtain more 'drug like' inhibitors with low micromolar activity. The preferred S-configuration of the capping residue can be explained by molecular modeling studies.
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Affiliation(s)
- Emanuela Nizi
- Department of Chemistry, IRBM, MRL Rome, Via Pontina Km 30,600, 00040 Pomezia, Rome, Italy
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42
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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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43
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Trozzi C, Bartholomew L, Ceccacci A, Biasiol G, Pacini L, Altamura S, Narjes F, Muraglia E, Paonessa G, Koch U, De Francesco R, Steinkuhler C, Migliaccio G. In vitro selection and characterization of hepatitis C virus serine protease variants resistant to an active-site peptide inhibitor. J Virol 2003; 77:3669-79. [PMID: 12610142 PMCID: PMC149541 DOI: 10.1128/jvi.77.6.3669-3679.2003] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [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: 11/06/2002] [Accepted: 12/13/2002] [Indexed: 01/08/2023] Open
Abstract
The hepatitis C virus (HCV) serine protease is necessary for viral replication and represents a valid target for developing new therapies for HCV infection. Potent and selective inhibitors of this enzyme have been identified and shown to inhibit HCV replication in tissue culture. The optimization of these inhibitors for clinical development would greatly benefit from in vitro systems for the identification and the study of resistant variants. We report the use HCV subgenomic replicons to isolate and characterize mutants resistant to a protease inhibitor. Taking advantage of the replicons' ability to transduce resistance to neomycin, we selected replicons with decreased sensitivity to the inhibitor by culturing the host cells in the presence of the inhibitor and neomycin. The selected replicons replicated to the same extent as those in parental cells. Sequence analysis followed by transfection of replicons containing isolated mutations revealed that resistance was mediated by amino acid substitutions in the protease. These results were confirmed by in vitro experiments with mutant enzymes and by modeling the inhibitor in the three-dimensional structure of the protease.
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44
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Narjes F, Koch U, Steinkühler C. Recent developments in the discovery of hepatitis C virus serine protease inhibitors--towards a new class of antiviral agents? Expert Opin Investig Drugs 2003; 12:153-63. [PMID: 12556211 DOI: 10.1517/13543784.12.2.153] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [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: 01/01/2023]
Abstract
Hepatitis C virus (HCV) infection is an epidemic disease and a significant worldwide health problem. Despite impressive improvements in the efficacy of the standard, interferon-based therapies, at present, the virus can not be eradicated in the majority of infected individuals. The last decade has witnessed a burst in our understanding of the molecular biology of HCV infection and lead to the identification of essential features of the viral genome that are being targeted for the development of specific antiviral agents. The non-structural protein 3 of the HCV genome harbours a serine protease domain that is essential for viral replication. This enzyme has been studied in great detail and the wealth of structural and functional data are presently nurturing drug development efforts. The peculiar active site structure of the enzyme imposes considerable obstacles to the development of small molecule inhibitors. However, the combination of creativity with the powerful tools of modern drug discovery has led to impressive progress in this field over the past few years and, as a result, the first compounds are now entering clinical trials.
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Affiliation(s)
- Frank Narjes
- Instituto di Ricerche di Biologia Molecolare-Merck Research Laboratories Rome,Via Pontina Km 30,600,00040 Pomezia, Italy
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45
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Colarusso S, Koch U, Gerlach B, Steinkühler C, De Francesco R, Altamura S, Matassa VG, Narjes F. Phenethyl amides as novel noncovalent inhibitors of hepatitis C virus NS3/4A protease: discovery, initial SAR, and molecular modeling. J Med Chem 2003; 46:345-8. [PMID: 12540231 DOI: 10.1021/jm025594q] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [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: 12/09/2022]
Abstract
The discovery of novel, reversible and competitive tripeptide inhibitors of the Hepatitis C virus NS3/4A serine protease is described. These inhibitors are characterized by the presence of a C-terminal phenethyl amide group, which extends into the prime side of the enzyme. Initial SAR together with molecular modeling and data from site-directed mutagenesis suggest an interaction of the phenethyl amide group with Lys-136.
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Affiliation(s)
- Stefania Colarusso
- Department of Chemistry, IRBM--MRL Rome, Via Pontina Km 30.600, 00040 Pomezia, Italy
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46
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Narjes F, Bolte O, Icheln D, Koenig WA, Schaumann E. Synthesis of vinylcyclopropanes by intramolecular epoxide ring opening. Application for an enantioselective synthesis of dictyopterene A. J Org Chem 2002. [DOI: 10.1021/jo00055a014] [Citation(s) in RCA: 29] [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: 11/28/2022]
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47
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48
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Colarusso S, Gerlach B, Koch U, Muraglia E, Conte I, Stansfield I, Matassa VG, Narjes F. Evolution, synthesis and SAR of tripeptide alpha-ketoacid inhibitors of the hepatitis C virus NS3/NS4A serine protease. Bioorg Med Chem Lett 2002; 12:705-8. [PMID: 11844706 DOI: 10.1016/s0960-894x(01)00843-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [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: 10/27/2022]
Abstract
N-terminal truncation of the hexapeptide ketoacid 1 gave rise to potent tripeptide inhibitors of the hepatitis C virus NS3 protease/NS4A cofactor complex. Optimization of these tripeptides led to ketoacid 30 with an IC50 of 0.38 microM. The SAR of these tripeptides is discussed in the light of the recently published crystal structures of a ternary tripetide/NS3/NS4A complexes.
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Affiliation(s)
- Stefania Colarusso
- Department of Chemistry, IRBM, MRL Rome, Via Pontina Km 30.600, Pomezia, 00040, Rome, Italy
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49
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Narjes F, Koehler KF, Koch U, Gerlach B, Colarusso S, Steinkühler C, Brunetti M, Altamura S, De Francesco R, Matassa VG. A designed P1 cysteine mimetic for covalent and non-covalent inhibitors of HCV NS3 protease. Bioorg Med Chem Lett 2002; 12:701-4. [PMID: 11844705 DOI: 10.1016/s0960-894x(01)00842-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 6.7] [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: 11/28/2022]
Abstract
The difluoromethyl group was designed by computational chemistry methods as a mimetic of the canonical P1 cysteine thiol for inhibitors of the hepatitis C virus NS3 protease. This modification led to the development of competitive, non-covalent inhibitor 4 (K(i) 30 nM) and reversible covalent inhibitors (6, K(i) 0.5 nM; and 8 K*(i) 10 pM).
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Affiliation(s)
- Frank Narjes
- Department of Chemistry, IRBM, MRL Rome, Via Pontina Km 30.600, Pomezia, 00040, Rome, Italy.
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50
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Pallaoro M, Lahm A, Biasiol G, Brunetti M, Nardella C, Orsatti L, Bonelli F, Orrù S, Narjes F, Steinkühler C. Characterization of the hepatitis C virus NS2/3 processing reaction by using a purified precursor protein. J Virol 2001; 75:9939-46. [PMID: 11559826 PMCID: PMC114565 DOI: 10.1128/jvi.75.20.9939-9946.2001] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2001] [Accepted: 07/23/2001] [Indexed: 01/12/2023] Open
Abstract
The NS2-NS3 region of the hepatitis C virus polyprotein encodes a proteolytic activity that is required for processing of the NS2/3 junction. Membrane association of NS2 and the autocatalytic nature of the NS2/3 processing event have so far constituted hurdles to the detailed investigation of this reaction. We now report the first biochemical characterization of the self-processing activity of a purified NS2/3 precursor. Using multiple sequence alignments, we were able to define a minimal domain, devoid of membrane-anchoring sequences, which was still capable of performing the processing reaction. This truncated protein was efficiently expressed and processed in Escherichia coli. The processing reaction could be significantly suppressed by growth in minimal medium in the absence of added zinc ions, leading to the accumulation of an unprocessed precursor protein in inclusion bodies. This protein was purified to homogeneity, refolded, and shown to undergo processing at the authentic NS2/NS3 cleavage site with rates comparable to those observed using an in vitro-translated full-length NS2/3 precursor. Size-exclusion chromatography and a dependence of the processing rate on the concentration of truncated NS2/3 suggested a functional multimerization of the precursor protein. However, we were unable to observe trans cleavage activity between cleavage-site mutants and active-site mutants. Furthermore, the cleavage reaction of the wild-type protein was not inhibited by addition of a mutant that was unable to undergo self-processing. Site-directed mutagenesis data and the independence of the processing rate from the nature of the added metal ion argue in favor of NS2/3 being a cysteine protease having Cys993 and His952 as a catalytic dyad. We conclude that a purified protein can efficiently reproduce processing at the NS2/3 site in the absence of additional cofactors.
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Affiliation(s)
- M Pallaoro
- Department of Biochemistry, Istituto di Ricerche di Biologia Molecolare "P. Angeletti," Pomezia, Italy
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