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Knodel MM, Nägel A, Herrmann E, Wittum G. Intracellular "In Silico Microscopes"-Comprehensive 3D Spatio-Temporal Virus Replication Model Simulations. Viruses 2024; 16:840. [PMID: 38932132 PMCID: PMC11209084 DOI: 10.3390/v16060840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/09/2024] [Accepted: 04/20/2024] [Indexed: 06/28/2024] Open
Abstract
Despite their small and simple structure compared with their hosts, virus particles can cause severe harm and even mortality in highly evolved species such as humans. A comprehensive quantitative biophysical understanding of intracellular virus replication mechanisms could aid in preparing for future virus pandemics. By elucidating the relationship between the form and function of intracellular structures from the host cell and viral components, it is possible to identify possible targets for direct antiviral agents and potent vaccines. Biophysical investigations into the spatio-temporal dynamics of intracellular virus replication have thus far been limited. This study introduces a framework to enable simulations of these dynamics using partial differential equation (PDE) models, which are evaluated using advanced numerical mathematical methods on leading supercomputers. In particular, this study presents a model of the replication cycle of a specific RNA virus, the hepatitis C virus. The diffusion-reaction model mimics the interplay of the major components of the viral replication cycle, including non structural viral proteins, viral genomic RNA, and a generic host factor. Technically, surface partial differential equations (sufPDEs) are coupled on the 3D embedded 2D endoplasmic reticulum manifold with partial differential equations (PDEs) in the 3D membranous web and cytosol volume. The membranous web serves as a viral replication factory and is formed on the endoplasmic reticulum after infection and in the presence of nonstructural proteins. The coupled sufPDE/PDE model was evaluated using realistic cell geometries based on experimental data. The simulations incorporate the effects of non structural viral proteins, which are restricted to the endoplasmic reticulum surface, with effects appearing in the volume, such as host factor supply from the cytosol and membranous web dynamics. Because the spatial diffusion properties of genomic viral RNA are not yet fully understood, the model allows for viral RNA movement on the endoplasmic reticulum as well as within the cytosol. Visualizing the simulated intracellular viral replication dynamics provides insights similar to those obtained by microscopy, complementing data from in vitro/in vivo viral replication experiments. The output data demonstrate quantitative consistence with the experimental findings, prompting further advanced experimental studies to validate the model and refine our quantitative biophysical understanding.
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Affiliation(s)
| | - Arne Nägel
- Modular Supercomputing and Quantum Computing (MSQC), Goethe-Universität Frankfurt, 60325 Frankfurt am Main, Germany;
| | - Eva Herrmann
- Institute for Biostatistics und Mathematical Modelling (IBMM), Goethe-Universität Frankfurt, 60590 Frankfurt am Main, Germany;
| | - Gabriel Wittum
- Modelling and Simulation (MaS), Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
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Knodel MM, Wittum G, Vollmer J. Efficient Estimates of Surface Diffusion Parameters for Spatio-Temporally Resolved Virus Replication Dynamics. Int J Mol Sci 2024; 25:2993. [PMID: 38474240 DOI: 10.3390/ijms25052993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Advanced methods of treatment are needed to fight the threats of virus-transmitted diseases and pandemics. Often, they are based on an improved biophysical understanding of virus replication strategies and processes in their host cells. For instance, an essential component of the replication of the hepatitis C virus (HCV) proceeds under the influence of nonstructural HCV proteins (NSPs) that are anchored to the endoplasmatic reticulum (ER), such as the NS5A protein. The diffusion of NSPs has been studied by in vitro fluorescence recovery after photobleaching (FRAP) experiments. The diffusive evolution of the concentration field of NSPs on the ER can be described by means of surface partial differential equations (sufPDEs). Previous work estimated the diffusion coefficient of the NS5A protein by minimizing the discrepancy between an extended set of sufPDE simulations and experimental FRAP time-series data. Here, we provide a scaling analysis of the sufPDEs that describe the diffusive evolution of the concentration field of NSPs on the ER. This analysis provides an estimate of the diffusion coefficient that is based only on the ratio of the membrane surface area in the FRAP region to its contour length. The quality of this estimate is explored by a comparison to numerical solutions of the sufPDE for a flat geometry and for ten different 3D embedded 2D ER grids that are derived from fluorescence z-stack data of the ER. Finally, we apply the new data analysis to the experimental FRAP time-series data analyzed in our previous paper, and we discuss the opportunities of the new approach.
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Affiliation(s)
- Markus M Knodel
- Simulation in Technology, TechSim, 75248 Ölbronn-Dürrn, Germany
| | - Gabriel Wittum
- Modelling and Simulation (MaS), Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jürgen Vollmer
- Institute for Theoretical Physics, Leipzig University, 04081 Leipzig, Germany
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Microscale Thermophoresis as a Tool to Study Protein Interactions and Their Implication in Human Diseases. Int J Mol Sci 2022; 23:ijms23147672. [PMID: 35887019 PMCID: PMC9315744 DOI: 10.3390/ijms23147672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 02/06/2023] Open
Abstract
The review highlights how protein–protein interactions (PPIs) have determining roles in most life processes and how interactions between protein partners are involved in various human diseases. The study of PPIs and binding interactions as well as their understanding, quantification and pharmacological regulation are crucial for therapeutic purposes. Diverse computational and analytical methods, combined with high-throughput screening (HTS), have been extensively used to characterize multiple types of PPIs, but these procedures are generally laborious, long and expensive. Rapid, robust and efficient alternative methods are proposed, including the use of Microscale Thermophoresis (MST), which has emerged as the technology of choice in drug discovery programs in recent years. This review summarizes selected case studies pertaining to the use of MST to detect therapeutically pertinent proteins and highlights the biological importance of binding interactions, implicated in various human diseases. The benefits and limitations of MST to study PPIs and to identify regulators are discussed.
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STAT1 and Its Crucial Role in the Control of Viral Infections. Int J Mol Sci 2022; 23:ijms23084095. [PMID: 35456913 PMCID: PMC9028532 DOI: 10.3390/ijms23084095] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
The signal transducer and activator of transcription (STAT) 1 protein plays a key role in the immune response against viruses and other pathogens by transducing, in the nucleus, the signal from type I, type II and type III IFNs. STAT1 activates the transcription of hundreds of genes, some of which have been well characterized for their antiviral properties. STAT1 gene deletion in mice and complete STAT1 deficiency in humans both cause rapid death from severe infections. STAT1 plays a key role in the immunoglobulin class-switch recombination through the upregulation of T-bet; it also plays a key role in the production of T-bet+ memory B cells that contribute to tissue-resident humoral memory by mounting an IgG response during re-infection. Considering the key role of STAT1 in the antiviral immune response, many viruses, including dangerous viruses such as Ebola and SARS-CoV-2, have developed different mechanisms to inhibit this transcription factor. The search for drugs capable of targeting the viral proteins implicated in both viral replication and IFN/STAT1 inhibition is important for the treatment of the most dangerous viral infections and for future viral pandemics, as shown by the clinical results obtained with Paxlovid in patients infected with SARS-CoV-2.
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Rehman AU, Zhen G, Zhong B, Ni D, Li J, Nasir A, Gabr MT, Rafiq H, Wadood A, Lu S, Zhang J, Chen HF. Mechanism of zinc ejection by disulfiram in nonstructural protein 5A. Phys Chem Chem Phys 2021; 23:12204-12215. [PMID: 34008604 DOI: 10.1039/d0cp06360f] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hepatitis C virus (HCV) is a notorious member of the Flaviviridae family of enveloped, positive-strand RNA viruses. Non-structural protein 5A (NS5A) plays a key role in HCV replication and assembly. NS5A is a multi-domain protein which includes an N-terminal amphipathic membrane anchoring alpha helix, a highly structured domain-1, and two intrinsically disordered domains 2-3. The highly structured domain-1 contains a zinc finger (Zf)-site, and binding of zinc stabilizes the overall structure, while ejection of this zinc from the Zf-site destabilizes the overall structure. Therefore, NS5A is an attractive target for anti-HCV therapy by disulfiram, through ejection of zinc from the Zf-site. However, the zinc ejection mechanism is poorly understood. To disclose this mechanism based on three different states, A-state (NS5A protein), B-state (NS5A + Zn), and C-state (NS5A + Zn + disulfiram), we have performed molecular dynamics (MD) simulation in tandem with DFT calculations in the current study. The MD results indicate that disulfiram triggers Zn ejection from the Zf-site predominantly through altering the overall conformation ensemble. On the other hand, the DFT assessment demonstrates that the Zn adopts a tetrahedral configuration at the Zf-site with four Cys residues, which indicates a stable protein structure morphology. Disulfiram binding induces major conformational changes at the Zf-site, introduces new interactions of Cys39 with disulfiram, and further weakens the interaction of this residue with Zn, causing ejection of zinc from the Zf-site. The proposed mechanism elucidates the therapeutic potential of disulfiram and offers theoretical guidance for the advancement of drug candidates.
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Affiliation(s)
- Ashfaq Ur Rehman
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 20025, China. and State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China and Department of Biochemistry, Abdul Wali Khan University Mardan, 23200, Pakistan.
| | - Guodong Zhen
- Department of VIP Clinic, Changhai Hospital, Navy Military Medical University, Shanghai, 200433, China
| | - Bozitao Zhong
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 20025, China.
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Abdul Nasir
- Synthetic Protein Engineering Lab, Molecular Science and Technology, Ajou University, Suwon 443-749, South Korea
| | - Moustafa T Gabr
- Department of Radiology, Stanford University, Stanford, California 94305, USA
| | - Humaira Rafiq
- Department of Biochemistry, Abdul Wali Khan University Mardan, 23200, Pakistan.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, 23200, Pakistan.
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 20025, China.
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 20025, China.
| | - Hai-Feng Chen
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 20025, China. and Shanghai Center for Bioinformation Technology, Shanghai, 200235, China
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Tarannum H, Chauhan B, Samadder A, Roy H, Nandi S. To Explore the Potential Targets and Current Structure-based Design Strategies Utilizing Co-crystallized Ligand to Combat HCV. Curr Drug Targets 2021; 22:590-604. [PMID: 32720601 DOI: 10.2174/1389450121999200727215020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatitis C Virus (HCV) belongs to the Hepacivirus family. HCV has been designated as a very dreadful virus as it can attack the liver, causing inflammation and even may lead to cancer in chronic conditions. It was estimated that 71 million people around the world have chronic HCV infection. World Health Organization (WHO) reported that about 399000 people died because of chronic cirrhosis and liver cancer globally. In spite of the abundance of availability of drugs for the treatment of HCV, however, the issue of drug resistance surpasses all the possibilities of therapeutic management of HCV. Therefore, to address this issue of 'drug-resistance', various HCV targets were explored to quest the evaluation of the mechanism of the disease progression. METHODS An attempt has been made in the present study to explore the various targets of HCV involved in the mechanism(s) of the disease initiation and progression and to focus on the mode of binding of ligands, which are co-crystallized at the active cavity of different HCV targets. CONCLUSION The present study could predict some crucial features of these ligands, which possibly interacted with various amino acid residues responsible for their biological activity and molecular signaling pathway(s). Such binding mode may be considered as a template for the high throughput screening and designing of active congeneric ligands to combat HCV.
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Affiliation(s)
- Heena Tarannum
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Bhumika Chauhan
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Andhra Pradesh, 522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
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Sinha A, Singh AK, Kadni TS, Mullick J, Sahu A. Virus-Encoded Complement Regulators: Current Status. Viruses 2021; 13:v13020208. [PMID: 33573085 PMCID: PMC7912105 DOI: 10.3390/v13020208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 11/29/2022] Open
Abstract
Viruses require a host for replication and survival and hence are subjected to host immunological pressures. The complement system, a crucial first response of the host immune system, is effective in targeting viruses and virus-infected cells, and boosting the antiviral innate and acquired immune responses. Thus, the system imposes a strong selection pressure on viruses. Consequently, viruses have evolved multiple countermeasures against host complement. A major mechanism employed by viruses to subvert the complement system is encoding proteins that target complement. Since viruses have limited genome size, most of these proteins are multifunctional in nature. In this review, we provide up to date information on the structure and complement regulatory functions of various viral proteins.
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Affiliation(s)
- Anwesha Sinha
- Complement Biology Laboratory, National Centre for Cell Science, S. P. Pune University Campus, Ganeskhind, Pune 411007, India; (A.S.); (A.K.S.); (T.S.K.)
| | - Anup Kumar Singh
- Complement Biology Laboratory, National Centre for Cell Science, S. P. Pune University Campus, Ganeskhind, Pune 411007, India; (A.S.); (A.K.S.); (T.S.K.)
| | - Trupti Satish Kadni
- Complement Biology Laboratory, National Centre for Cell Science, S. P. Pune University Campus, Ganeskhind, Pune 411007, India; (A.S.); (A.K.S.); (T.S.K.)
| | - Jayati Mullick
- Polio Virology Group, Microbial Containment Complex, ICMR-National Institute of Virology, Pune 411021, India;
| | - Arvind Sahu
- Complement Biology Laboratory, National Centre for Cell Science, S. P. Pune University Campus, Ganeskhind, Pune 411007, India; (A.S.); (A.K.S.); (T.S.K.)
- Correspondence: ; Tel.: +91-20-2570-8083; Fax: +91-20-2569-2259
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Synthesis, biological evaluation and in silico modeling of novel pan-genotypic NS5A inhibitors. Bioorg Med Chem 2020; 28:115716. [PMID: 33069072 DOI: 10.1016/j.bmc.2020.115716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/07/2020] [Accepted: 08/16/2020] [Indexed: 01/01/2023]
Abstract
A series of novel small-molecule pan-genotypic hepatitis C virus (HCV) NS5A inhibitors with picomolar activity containing 2-[(2S)-pyrrolidin-2-yl]-5-[4-(4-{2-[(2S)-pyrrolidin-2-yl]-1H-imidazol-5-yl}buta-1,3-diyn-1-yl)phenyl]-1H-imidazole core was designed based on molecular modeling study and SAR analysis. The constructed in silico model and docking study provide a deep insight into the binding mode of this type of NS5A inhibitors. Based on the predicted binding interface we have prioritized the most crucial diversity points responsible for improving antiviral activity. The synthesized molecules were tested in a cell-based assay, and compound 1.12 showed an EC50 value in the range of 2.9-34 pM against six genotypes of NS5A HCV, including gT3a, and demonstrated favorable pharmacokinetic profile in rats. This lead compound can be considered as an attractive candidate for further clinical evaluation.
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Sofia MJ. The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex. ACTA ACUST UNITED AC 2019. [PMCID: PMC7122418 DOI: 10.1007/7355_2018_47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Knodel MM, Targett-Adams P, Grillo A, Herrmann E, Wittum G. Advanced Hepatitis C Virus Replication PDE Models within a Realistic Intracellular Geometric Environment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E513. [PMID: 30759770 PMCID: PMC6388173 DOI: 10.3390/ijerph16030513] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/08/2019] [Accepted: 01/16/2019] [Indexed: 02/06/2023]
Abstract
The hepatitis C virus (HCV) RNA replication cycle is a dynamic intracellular process occurring in three-dimensional space (3D), which is difficult both to capture experimentally and to visualize conceptually. HCV-generated replication factories are housed within virus-induced intracellular structures termed membranous webs (MW), which are derived from the Endoplasmatic Reticulum (ER). Recently, we published 3D spatiotemporal resolved diffusion⁻reaction models of the HCV RNA replication cycle by means of surface partial differential equation (sPDE) descriptions. We distinguished between the basic components of the HCV RNA replication cycle, namely HCV RNA, non-structural viral proteins (NSPs), and a host factor. In particular, we evaluated the sPDE models upon realistic reconstructed intracellular compartments (ER/MW). In this paper, we propose a significant extension of the model based upon two additional parameters: different aggregate states of HCV RNA and NSPs, and population dynamics inspired diffusion and reaction coefficients instead of multilinear ones. The combination of both aspects enables realistic modeling of viral replication at all scales. Specifically, we describe a replication complex state consisting of HCV RNA together with a defined amount of NSPs. As a result of the combination of spatial resolution and different aggregate states, the new model mimics a cis requirement for HCV RNA replication. We used heuristic parameters for our simulations, which were run only on a subsection of the ER. Nevertheless, this was sufficient to allow the fitting of core aspects of virus reproduction, at least qualitatively. Our findings should help stimulate new model approaches and experimental directions for virology.
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Affiliation(s)
- Markus M Knodel
- Department of Mathematics, Chair of Applied Mathematics 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 11, 91058 Erlangen, Germany.
| | | | - Alfio Grillo
- Dipartimento di Scienze Matematiche (DISMA) "G.L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129 Torino (TO), Italy.
| | - Eva Herrmann
- Department of Medicine, Institute for Biostatistics and Mathematic Modeling, Goethe Universität Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Gabriel Wittum
- Goethe Center for Scientific Computing (G-CSC), Goethe Universität Frankfurt, Kettenhofweg 139, 60325 Frankfurt am Main, Germany.
- Applied Mathematics and Computational Science, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia.
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Schwartz N, Pellach M, Glick Y, Gil R, Levy G, Avrahami D, Barbiro-Michaely E, Nahmias Y, Gerber D. Neuregulin 1 discovered as a cleavage target for the HCV NS3/4A protease by a microfluidic membrane protein array. N Biotechnol 2018; 45:113-122. [PMID: 29438748 DOI: 10.1016/j.nbt.2018.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 12/26/2022]
Abstract
The hepatitis C virus (HCV) non-structural protein 3 (NS3) is essential for HCV maturation. The NS3/4A protease is a target for several HCV treatments and is a well-known target for HCV drug discovery. The protein is membrane associated and thus probably interacts with other membrane proteins. However, the vast majority of known NS3 host partners are soluble proteins rather than membrane proteins, most likely due to lack of appropriate platforms for their discovery. Utilization of an integrated microfluidics platform enables analysis of membrane proteins in their native form. We screened over 2800 membrane proteins for interaction with NS3 and 90 previously unknown interactions were identified. Of these, several proteins were selected for validation by co-immunoprecipitation and for NS3 proteolytic activity. Bearing in mind the considerable number of interactions formed, together with the popularity of NS3/4A protease as a drug target, it was striking to note its lack of proteolytic activity. Only a single protein, Neuregulin1, was observed to be cleaved, adding to the 3 known NS3/4A cleavage targets. Neuregulin1 participates in neural proliferation. Recent studies have shown its involvement in HCV infection and hepatocellular carcinoma. We showed that NS3/4A triggers an increase in neuregulin1 mRNA levels in HCV infected cells. Despite this increase, its protein concentration is decreased due to proteolytic cleavage. Additionally, its EGF-like domain levels were increased, possibly explaining the ErbB2 and EGFR upregulation in HCV infected cells. The newly discovered protein interactions may provide insights into HCV infection mechanisms and potentially provide new therapeutic targets against HCV.
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Affiliation(s)
- Nika Schwartz
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Michal Pellach
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Yair Glick
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Reuven Gil
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Gahl Levy
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dorit Avrahami
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Efrat Barbiro-Michaely
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Yaakov Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doron Gerber
- Mina and Everard Goodman Faculty of Life Sciences and Bar Ilan Institute for Nanotechnology and Advanced Materials, Anna Web Nanotechnology bld. (206), Bar Ilan University, Ramat Gan, 5290002, Israel.
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Quantitative Analysis of Hepatitis C NS5A Viral Protein Dynamics on the ER Surface. Viruses 2018; 10:v10010028. [PMID: 29316722 PMCID: PMC5795441 DOI: 10.3390/v10010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.
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Kinoshita K, Iwasa T, Asante-Appiah E, Nakamura K. Preclinical and clinical properties of elbasvir (ERELSA ® Tablets 50 mg) and Grazoprevir (GRAZYNA ® Tablets 50 mg), novel therapeutic agents for hepatitis C. Nihon Yakurigaku Zasshi 2017; 150:41-53. [PMID: 28690275 DOI: 10.1254/fpj.150.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Glab-Ampai K, Chulanetra M, Malik AA, Juntadech T, Thanongsaksrikul J, Srimanote P, Thueng-In K, Sookrung N, Tongtawe P, Chaicumpa W. Human single chain-transbodies that bound to domain-I of non-structural protein 5A (NS5A) of hepatitis C virus. Sci Rep 2017; 7:15042. [PMID: 29118372 PMCID: PMC5678119 DOI: 10.1038/s41598-017-14886-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/18/2017] [Indexed: 12/15/2022] Open
Abstract
A safe and broadly effective direct acting anti-hepatitis C virus (HCV) agent that can withstand the viral mutation is needed. In this study, human single chain antibody variable fragments (HuscFvs) to conserved non-structural protein-5A (NS5A) of HCV were produced by phage display technology. Recombinant NS5A was used as bait for fishing-out the protein bound-phages from the HuscFv-phage display library. NS5A-bound HuscFvs produced by five phage transfected-E. coli clones were linked molecularly to nonaarginine (R9) for making them cell penetrable (become transbodies). The human monoclonal transbodies inhibited HCV replication in the HCVcc infected human hepatic cells and also rescued the cellular antiviral immune response from the viral suppression. Computerized simulation verified by immunoassays indicated that the transbodies used several residues in their multiple complementarity determining regions (CDRs) to form contact interface with many residues of the NS5A domain-I which is important for HCV replication complex formation and RNA binding as well as for interacting with several host proteins for viral immune evasion and regulation of cellular physiology. The human monoclonal transbodies have high potential for testing further as a new ramification of direct acting anti-HCV agent, either alone or in combination with their cognates that target other HCV proteins.
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Affiliation(s)
- Kittirat Glab-Ampai
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Monrat Chulanetra
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Aijaz Ahmad Malik
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thanate Juntadech
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jeeraphong Thanongsaksrikul
- Graduate Program in Biomedical Science, Faculty of Allied Health Sciences, Thammasat University, Rangsit Campus, Pathum-thani province, 12120, Thailand
| | - Potjanee Srimanote
- Graduate Program in Biomedical Science, Faculty of Allied Health Sciences, Thammasat University, Rangsit Campus, Pathum-thani province, 12120, Thailand
| | - Kanyarat Thueng-In
- School of Pathology, Institute of Medicine, Suranaree University of Technology, Nakhon-ratchaseema province, Thailand
| | - Nitat Sookrung
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pongsri Tongtawe
- Graduate Program in Biomedical Science, Faculty of Allied Health Sciences, Thammasat University, Rangsit Campus, Pathum-thani province, 12120, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
- Graduate Program in Biomedical Science, Faculty of Allied Health Sciences, Thammasat University, Rangsit Campus, Pathum-thani province, 12120, Thailand.
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16
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Mehmood A, Asad MJ, Ovais M, Zaman N, Aziz H, Irfan J, Ahmad I, Raza A. The Absence of HCV RNA and NS5A Protein in Peripheral Blood Mononuclear Cells Is a Prognostic Tool for Sustained Virological Response. Viral Immunol 2017; 30:568-575. [DOI: 10.1089/vim.2017.0030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Azhar Mehmood
- Nuclear Medicine, Oncology, and Radiotherapy, Institute NORI, Islamabad, Pakistan
- Department of Biochemistry, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Javaid Asad
- Department of Biochemistry, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Ovais
- Nuclear Medicine, Oncology, and Radiotherapy, Institute NORI, Islamabad, Pakistan
| | - Nasib Zaman
- Department of Biochemistry, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Hafsa Aziz
- Nuclear Medicine, Oncology, and Radiotherapy, Institute NORI, Islamabad, Pakistan
| | - Javaid Irfan
- Nuclear Medicine, Oncology, and Radiotherapy, Institute NORI, Islamabad, Pakistan
| | - Irshad Ahmad
- Department of Life Sciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia
| | - Abida Raza
- Nuclear Medicine, Oncology, and Radiotherapy, Institute NORI, Islamabad, Pakistan
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17
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3D Spatially Resolved Models of the Intracellular Dynamics of the Hepatitis C Genome Replication Cycle. Viruses 2017; 9:v9100282. [PMID: 28973992 PMCID: PMC5691296 DOI: 10.3390/v9100282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/21/2017] [Accepted: 09/29/2017] [Indexed: 02/07/2023] Open
Abstract
Mathematical models of virus dynamics have not previously acknowledged spatial resolution at the intracellular level despite substantial arguments that favor the consideration of intracellular spatial dependence. The replication of the hepatitis C virus (HCV) viral RNA (vRNA) occurs within special replication complexes formed from membranes derived from endoplasmatic reticulum (ER). These regions, termed membranous webs, are generated primarily through specific interactions between nonstructural virus-encoded proteins (NSPs) and host cellular factors. The NSPs are responsible for the replication of the vRNA and their movement is restricted to the ER surface. Therefore, in this study we developed fully spatio-temporal resolved models of the vRNA replication cycle of HCV. Our simulations are performed upon realistic reconstructed cell structures-namely the ER surface and the membranous webs-based on data derived from immunostained cells replicating HCV vRNA. We visualized 3D simulations that reproduced dynamics resulting from interplay of the different components of our models (vRNA, NSPs, and a host factor), and we present an evaluation of the concentrations for the components within different regions of the cell. Thus far, our model is restricted to an internal portion of a hepatocyte and is qualitative more than quantitative. For a quantitative adaption to complete cells, various additional parameters will have to be determined through further in vitro cell biology experiments, which can be stimulated by the results deccribed in the present study.
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18
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Jin G, Lee J, Lee K. Chemical genetics-based development of small molecules targeting hepatitis C virus. Arch Pharm Res 2017; 40:1021-1036. [PMID: 28856597 DOI: 10.1007/s12272-017-0949-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/20/2017] [Indexed: 12/21/2022]
Abstract
Hepatitis C virus (HCV) infection is a major worldwide problem that has emerged as one of the most significant diseases affecting humans. There are currently no vaccines or efficient therapies without side effects, despite today's advanced medical technology. Currently, the common therapy for most patients (i.e. genotype 1) is combination of HCV-specific direct-acting antivirals (DAAs). Up to 2011, the standard of care (SOC) was a combination of peg-IFNα with ribavirin (RBV). After approval of NS3/4A protease inhibitor, SOC was peg-IFNα and RBV with either the first-generation DAAs boceprevir or telaprevir. In the past several years, various novel small molecules have been discovered and some of them (i.e., HCV polymerase, protease, helicase and entry inhibitors) have undergone clinical trials. Between 2013 and 2016, the second-generation DAA drugs simeprevir, asunaprevir, daclatasvir, dasabuvir, sofosbuvir, and elbasvir were approved, as well as the combinational drugs Harvoni®, Zepatier®, Technivie®, and Epclusa®. A number of reviews have been recently published describing the structure-activity relationship (SAR) in the development of HCV inhibitors and outlining current therapeutic approaches to hepatitis C infection. Target identification involves studying a drug's mechanism of action (MOA), and a variety of target identification methods have been developed in the past few years. Chemical biology has emerged as a powerful tool for studying biological processes using small molecules. The use of chemical genetic methods is a valuable strategy for studying the molecular mechanisms of the viral lifecycle and screening for anti-viral agents. Two general screening approaches have been employed: forward and reverse chemical genetics. This review reveals information on the small molecules in HCV drug discovery by using chemical genetics for targeting the HCV protein and describes successful examples of targets identified with these methods.
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Affiliation(s)
- Guanghai Jin
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jisu Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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19
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Gamal N, Gitto S, Andreone P. Efficacy and Safety of Daclatasvir in Hepatitis C: An Overview. J Clin Transl Hepatol 2016; 4:336-344. [PMID: 28097103 PMCID: PMC5225154 DOI: 10.14218/jcth.2016.00038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a growing public health concern, with 184 million people infected worldwide. During the past decade, interferon has been the backbone of HCV treatment, even though it remains far from ideal. The latest development of the new direct antivirals has drastically changed the treatment approach for chronic hepatitis C (CHC). Inhibitors of the HCV NS5A region have garnered remarkable interest among treating physicians, due to their high potency and favourable safety profile. In particular, treatment with daclatasvir (DCV) has yielded high rates of vriologic response in patients infected with genotype (Gt) 1 and Gt 3, when used in combination with other antivirals of a different class, such as sofosbuvir. Although few data are available for DCV treatment of the other Gts, the results in patients with Gt 2 and Gt 4 infection appear promising, as do those for unique patient populations. NS5A-resistant viral variants can pre-exist or emerge after treatment failure for the HCV NS5A inhibitors. Nonetheless, DCV-resistant viral variants continue to be sensitive to interferon and other classes of antivirals such as NS3/4A and NS5B inhibitors. Herein, we aimed to provide an overview of the current knowledge about DCV in the treatment of CHC.
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Affiliation(s)
- Nesrine Gamal
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Stefano Gitto
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Pietro Andreone
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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20
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Tong L, Yu W, Chen L, Selyutin O, Dwyer MP, Nair AG, Mazzola R, Kim JH, Sha D, Yin J, Ruck RT, Davies IW, Hu B, Zhong B, Hao J, Ji T, Zan S, Liu R, Agrawal S, Xia E, Curry S, McMonagle P, Bystol K, Lahser F, Carr D, Rokosz L, Ingravallo P, Chen S, Feng KI, Cartwright M, Asante-Appiah E, Kozlowski JA. Discovery of Ruzasvir (MK-8408): A Potent, Pan-Genotype HCV NS5A Inhibitor with Optimized Activity against Common Resistance-Associated Polymorphisms. J Med Chem 2016; 60:290-306. [PMID: 27808515 DOI: 10.1021/acs.jmedchem.6b01310] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We describe the research that led to the discovery of compound 40 (ruzasvir, MK-8408), a pan-genotypic HCV nonstructural protein 5A (NS5A) inhibitor with a "flat" GT1 mutant profile. This NS5A inhibitor contains a unique tetracyclic indole core while maintaining the imidazole-proline-valine Moc motifs of our previous NS5A inhibitors. Compound 40 is currently in early clinical trials and is under evaluation as part of an all-oral DAA regimen for the treatment of chronic HCV infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Bin Hu
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Bin Zhong
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Jinglai Hao
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Tao Ji
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
| | - Shuai Zan
- Department of Medicinal Chemistry, WuXi AppTec , Shanghai, 200131, China
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21
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Ooka K, Lim JK. Treatment of Hepatitis C in Patients Undergoing Immunosuppressive Drug Therapy. J Clin Transl Hepatol 2016; 4:206-227. [PMID: 27777889 PMCID: PMC5075004 DOI: 10.14218/jcth.2016.00017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/22/2016] [Accepted: 07/12/2016] [Indexed: 12/09/2022] Open
Abstract
With 185 million people chronically infected globally, hepatitis C is a leading bloodborne infection. All-oral regimens of direct acting agents have superior efficacy compared to the historical interferon-based regimens and are significantly more tolerable. However, trials of both types of regimens have often excluded patients on immunosuppressive medications for reasons other than organ transplantation. Yet, these patients-most often suffering from malignancy or autoimmune diseases-could stand to benefit from these treatments. In this study, we systematically review the literature on the treatment of hepatitis C in these neglected populations. Research on patients with organ transplants is more robust and this literature is reviewed here non-systematically. Our systematic review produced 2273 unique works, of which 56 met our inclusion criteria and were used in our review. The quality of data was low; only 3 of the 56 studies were randomized controlled trials. Sustained virologic response was reported sporadically. Interferon-containing regimens achieved this end-point at rates comparable to that in immunocompetent individuals. Severe adverse effects and death were rare. Data on all-oral regimens were sparse, but in the most robust study, rates of sustained virologic response were again comparable to immunocompetent individuals (40/41). Efficacy and safety of interferon-containing regimens and all-oral regimens were similar to rates in immunocompetent individuals; however, there were few interventional trials. The large number of case reports and case series makes conclusions vulnerable to publication bias. While firm conclusions are challenging, given the dearth of high-quality studies, our results demonstrate that antiviral therapy can be safe and effective. The advent of all-oral regimens offers patients and clinicians greatly increased chances of cure and fewer side effects. Preliminary data reveal that these regimens may confer such benefits in immunosuppressed individuals as well. More prospective interventional trials would greatly benefit the many patients with chronic hepatitis C on immunosuppressive therapies.
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Affiliation(s)
- Kohtaro Ooka
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph K. Lim
- Yale Liver Center, Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA
- *Correspondence to: Joseph K. Lim, Yale Liver Center, Section of Digestive Diseases, Yale University School of Medicine, 333 Cedar Street, LMP 1080, New Haven, CT 06520-8019, USA. Tel: +1-203-737-6063, Fax: +1-203-785-7273, E-mail:
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22
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Tong L, Yu W, Coburn CA, Chen L, Selyutin O, Zeng Q, Dwyer MP, Nair AG, Shankar BB, Kim SH, Yang DY, Rosenblum SB, Ruck RT, Davies IW, Hu B, Zhong B, Hao J, Ji T, Zan S, Liu R, Agrawal S, Carr D, Curry S, McMonagle P, Bystol K, Lahser F, Ingravallo P, Chen S, Asante-Appiah E, Kozlowski JA. Structure-activity relationships of proline modifications around the tetracyclic-indole class of NS5A inhibitors. Bioorg Med Chem Lett 2016; 26:5354-5360. [PMID: 27680588 DOI: 10.1016/j.bmcl.2016.08.097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/31/2016] [Indexed: 01/26/2023]
Abstract
We describe the impact of proline modifications, in our tetracyclic-indole based series of nonstructural protein 5A (NS5A) inhibitors, to their replicon profiles. This work identified NS5A inhibitors with an improved and flattened resistance profiles.
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Affiliation(s)
- Ling Tong
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA.
| | - Wensheng Yu
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Craig A Coburn
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Lei Chen
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Oleg Selyutin
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Qingbei Zeng
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Michael P Dwyer
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | | | | | - Seong Heon Kim
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - De-Yi Yang
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | | | - Rebecca T Ruck
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Ian W Davies
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Bin Hu
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Bin Zhong
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Jinglai Hao
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Tao Ji
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Shuai Zan
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Rong Liu
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Sony Agrawal
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Donna Carr
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Stephanie Curry
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | | | - Karin Bystol
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | | | - Paul Ingravallo
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Shiying Chen
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
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23
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Tong L, Yu W, Coburn CA, Meinke PT, Nair AG, Dwyer MP, Chen L, Selyutin O, Rosenblum SB, Jiang Y, Fells J, Hu B, Zhong B, Soll RM, Liu R, Agrawal S, Xia E, Zhai Y, Kong R, Ingravallo P, Nomeir A, Asante-Appiah E, Kozlowski JA. Alternative core development around the tetracyclic indole class of HCV NS5A inhibitors. Bioorg Med Chem Lett 2016; 26:5132-5137. [PMID: 27634194 DOI: 10.1016/j.bmcl.2016.07.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 07/22/2016] [Accepted: 07/23/2016] [Indexed: 01/17/2023]
Abstract
Herein, we describe our research efforts to develop unique cores in molecules which function as HCV nonstructural protein 5A (NS5A) inhibitors. In particular, various fused tetracyclic cores were identified which showed genotype and mutant activities comparable to the indole-based tetracyclic core.
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Affiliation(s)
- Ling Tong
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Wensheng Yu
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Craig A Coburn
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Peter T Meinke
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Anilkumar G Nair
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Michael P Dwyer
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Lei Chen
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Oleg Selyutin
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | | | - Yueheng Jiang
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - James Fells
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Bin Hu
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Bin Zhong
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Richard M Soll
- Department of Medicinal Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Rong Liu
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Sony Agrawal
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Ellen Xia
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Ying Zhai
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Rong Kong
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Paul Ingravallo
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Amin Nomeir
- Merck Research Laboratories, 126 E. Lincoln Ave., Rahway, NJ 07065, USA
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Abstract
Antiviral therapeutics with profiles of high potency, low resistance, panserotype, and low toxicity remain challenging, and obtaining such agents continues to be an active area of therapeutic development. Due to their unique three-dimensional structural features, spirooxindoles have been identified as privileged chemotypes for antiviral drug development. Among them, spiro-pyrazolopyridone oxindoles have been recently reported as potent inhibitors of dengue virus NS4B, leading to the discovery of an orally bioavailable preclinical candidate (R)-44 with excellent in vivo efficacy in a dengue viremia mouse model. This review highlights recent advances in the development of biologically active spirooxindoles for their antiviral potential, primarily focusing on the structure-activity relationships (SARs) and modes of action, as well as future directions to achieve more potent analogues toward a viable antiviral therapy.
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Affiliation(s)
- Na Ye
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Eric A. Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Pei-Yong Shi
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
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25
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Abstract
INTRODUCTION The direct acting antiviral daclatasvir is an NS5A replication inhibitor active against the entire range of hepatitis C virus genotypes. It is a key step in establishing the goal of an all-oral, ribavirin-free, pan-genotypic regimen against hepatitis C. AREAS COVERED We review current literature including published abstracts and manuscripts. Evidence was obtained through PubMed/Medline search using listed keywords and through review of published abstracts. EXPERT OPINION Daclatasvir introduces a degree of pangenotypic potency currently lacking in other NS5A agents. Emerging literature suggests that daclatasvir in combination with other DAAs will represent a promising option in this difficult to treat populations including posttransplant, genotype 3 and HIV patients.
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Affiliation(s)
- Syed-Mohammed Jafri
- a Division of Gastroenterology , Henry Ford Hospital , Detroit , MI 48202 , USA
| | - Stuart C Gordon
- a Division of Gastroenterology , Henry Ford Hospital , Detroit , MI 48202 , USA
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26
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Majumdar A, Kitson MT, Roberts SK. Systematic review: current concepts and challenges for the direct-acting antiviral era in hepatitis C cirrhosis. Aliment Pharmacol Ther 2016; 43:1276-92. [PMID: 27087015 DOI: 10.1111/apt.13633] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/06/2015] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND The burden of HCV cirrhosis is high and projected to increase significantly over the next decade. While interferon therapy is problematic in HCV cirrhosis, the era of direct-acting anti-viral (DAA) therapy provides effective treatment for patients with cirrhosis. AIM To systematically review the results of DAA therapy to date in patients with HCV cirrhosis, and highlight the ongoing challenges for DAA therapy in this population. METHODS A structured Medline search was conducted to obtain phase II and III HCV trials in patients with cirrhosis. Citations from review articles were cross-referenced and conference abstracts from EASL and AASLD liver meetings for the preceding 3 years were reviewed manually. Keywords used included hepatitis C, cirrhosis and the DAA's: sofosbuvir, ledipasvir, velpatasvir, grazoprevir, elbasvir, daclatasvir, beclabuvir, asunaprevir, simeprevir, paritaprevir, ombitasvir and dasabuvir. RESULTS Successful direct-acting anti-viral treatment is now possible in patients with HCV-related cirrhosis including those with liver decompensation with several regimens now offering sustained virological response (SVR) of 90-95%. Overall success rates in GT1 cirrhosis are excellent while GT3-infected patients with cirrhosis remain hard to cure. The pangenotypic combination of sofosbuvir and velpatasvir holds promise for GT3 cirrhosis achieving SVR of ~90%. CONCLUSIONS Potent DAA therapies provide much needed, safe and highly effective treatment options for persons with HCV cirrhosis including those previously deemed unsuitable for treatment. Combination therapy with two or more classes of drug is essential to achieve high efficacy and minimise viral resistance, with the role of ribavirin still under evaluation. However, several challenges remain including the hard-to-cure groups of GT3 cirrhosis and direct-acting anti-viral failures, and managing drug-drug interactions.
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Affiliation(s)
- A Majumdar
- Department of Gastroenterology, Alfred Hospital, Melbourne, Vic., Australia.,UCL Institute for Liver and Digestive Health and Sheila Sherlock Liver Centre Royal Free Hospital, London, UK
| | - M T Kitson
- Department of Gastroenterology, Alfred Hospital, Melbourne, Vic., Australia
| | - S K Roberts
- Department of Gastroenterology, Alfred Hospital, Melbourne, Vic., Australia
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Kwo PY, Badshah MB. Treatment of HCV in Patients who Failed First-Generation PI Therapy: a Review of Current Literature. Curr Gastroenterol Rep 2016; 17:462. [PMID: 26342813 DOI: 10.1007/s11894-015-0462-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The addition of the first direct-acting antiviral agents, the NS3 protease inhibitors boceprevir or telaprevir, to peg interferon and ribavirin was a major advance in the treatment of genotype 1 hepatitis C individuals with sustained virological response (SVR) rates of 63-75 %. Those who did not achieve SVR had high rates of resistance-associated variants against NS3 protease domain. Retreatment options for those who have failed first-generation protease inhibitors generally are guided by retreatment with direct-acting antiviral agents from other classes. Phase 2 and phase 3 data have demonstrated that retreatment with 12-24 weeks of a NS5B inhibitor (sofosbuvir) in combination with a NS5a inhibitor (daclatasvir or ledipasvir) with or without ribavirin can achieve SVR at high rates comparable to treatment-naive individuals.
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Affiliation(s)
- Paul Y Kwo
- Department of Medicine, Division of Gastroenterology/Hepatology, Indiana University School of Medicine, 975 W. Walnut, IB 327, Indianapolis, IN, 46202-5121, USA,
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Lee YM, Duh Y, Wang ST, Lai MMC, Yuan HS, Lim C. Using an Old Drug to Target a New Drug Site: Application of Disulfiram to Target the Zn-Site in HCV NS5A Protein. J Am Chem Soc 2016; 138:3856-62. [PMID: 26928525 DOI: 10.1021/jacs.6b00299] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In viral proteins, labile Zn-sites, where Zn(2+) is crucial for maintaining the native protein structure but the Zn-bound cysteines are reactive, are promising drug targets. Here, we aim to (i) identify labile Zn-sites in viral proteins using guidelines established from our previous work and (ii) assess if clinically safe Zn-ejecting agents could eject Zn(2+) from the predicted target site and thus inhibit viral replication. As proof-of-concept, we identified a labile Zn-site in the hepatitis C virus (HCV) NS5A protein and showed that the antialcoholism drug, disulfiram, could inhibit HCV replication to a similar extent as the clinically used antiviral agent, ribavirin. The discovery of a novel viral target and a new role for disulfiram in inhibiting HCV replication will enhance the therapeutic armamentarium against HCV. The strategy presented can also be applied to identify labile sites in other bacterial or viral proteins that can be targeted by disulfiram or other clinically safe Zn-ejectors.
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Affiliation(s)
- Yu-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan
| | - Yulander Duh
- Institute of Molecular Biology, Academia Sinica , Taipei 115, Taiwan
| | - Shih-Ting Wang
- Institute of Molecular Biology, Academia Sinica , Taipei 115, Taiwan
| | - Michael M C Lai
- Institute of Molecular Biology, Academia Sinica , Taipei 115, Taiwan
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica , Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
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Treatment of hepatitis C in patients with cirrhosis: remaining challenges for direct-acting antiviral therapy. Drugs 2016; 75:823-34. [PMID: 25943281 DOI: 10.1007/s40265-015-0401-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chronic hepatitis C virus (HCV) infection is a major global health concern, resulting in significant morbidity and mortality. Treatment using interferon-based therapy in patients with HCV-related cirrhosis has been problematic due to toxicity and poor tolerability. Furthermore, interferon therapy is contraindicated in those with advanced cirrhosis or clinical decompensation, who are arguably the group most in need of viral eradication. The arrival of the direct-acting antiviral (DAA) era has resulted in the development of well-tolerated and highly effective interferon-free drug regimens that promise to dramatically change the therapeutic landscape for those with advanced HCV-related liver disease, including patients with clinical decompensation or pre-liver transplantation. Many successful DAA combinations have emerged; however, a number of challenges remain including the establishment of the optimal treatment duration, the ideal combination of drug classes and determining the role of ribavirin. Moreover, the identification of treatment-experienced patients with genotype 3 HCV cirrhosis as a difficult-to-treat subgroup is a significant impediment to overcome, as are those who have failed prior DAA therapy. Despite these barriers, the ongoing prolific development of safe and effective DAA combinations indicates the future is optimistic for the ultimate goal of HCV eradication.
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Discovery of silyl proline containing HCV NS5A inhibitors with pan-genotype activity: SAR development. Bioorg Med Chem Lett 2016; 26:1475-9. [PMID: 26850003 DOI: 10.1016/j.bmcl.2016.01.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 01/26/2023]
Abstract
HCV NS5A inhibitors have shown impressive in vitro potency profiles in HCV replicon assays thus making them attractive components for inclusion in an all oral fixed dose combination treatment regimen. Herein we describe the research efforts that led to the discovery of silyl proline containing HCV NS5A inhibitors such as 7e and 8a with pan-genotype activity profile and acceptable pharmacokinetic properties.
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New hepatitis C virus therapies: drug classes and metabolism, drug interactions relevant in the transplant settings, drug options in decompensated cirrhosis, and drug options in end-stage renal disease. Curr Opin Organ Transplant 2015; 20:235-41. [PMID: 25944238 DOI: 10.1097/mot.0000000000000198] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE OF REVIEW This article will review the new direct acting antiviral agent (DAA) drug classes for the treatment of hepatitis C, how they are combined and the relevant drug-drug interactions in the postliver transplant setting. Treatment options for chronic hepatitis C in patients with decompensated cirrhosis and end-stage renal disease will also be discussed. RECENT FINDINGS The availability of new drug classes has increased the treatment options in patients with hepatitis C in the post-transplant settings. Clinical trials have concluded that sofosbuvir (SOF) with ledipasvir (LDV) may be safely administered with calcineurin inhibitors (tacrolimus, cyclosporine) and rapamycin inhibitors (sirolimus, everolimus). Similarly, paritaprevir/ritonavir, ombitasvir, and dasabuvir may be administered with tacrolimus and cyclosporine though appropriate dose adjustments must be made to the calcineurin inhibitors. In those with decompensated Childs B/C cirrhosis, SOF, SOF and LDV, as well as daclatasvir may be given without dose adjustment. In renal impairment, all DAAs may be used safely down to a glomerular filteration rate (GFR) of 30 ml/min. Simeprevir, paritaprevir, ombitasvir, and dasabuvir may be given for those down to GFR of 15 ml/min. Finally, daclatasvir may be given without dose administration change. SUMMARY In summary, DAAs have better tolerability and greater efficacy than interferon-based therapy post-transplant. Drug-drug interactions must be carefully assessed when these newer agents are used for therapy in the postliver transplant settings. Thus far, dose adjustments for DAAs have not been required in chronic kidney disease though data are incomplete in those with severe chronic kidney disease (CKD) or on dialysis. Hepatitis C treatment in those with decompensated cirrhosis results in impaired hepatic metabolism that may affect DAA levels, and clinicians should carefully choose treatment options for Childs B and C cirrhotic patients.
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Aghemo A, De Francesco R. Daclatasvir: a team player rather than a prima donna in the treatment of hepatitis C. Gut 2015; 64:860-2. [PMID: 25193803 DOI: 10.1136/gutjnl-2014-307958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 08/19/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Alessio Aghemo
- Division of Gastroenterology and Hepatology, A.M. and A. Migliavacca Center for Liver Disease, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Raffaele De Francesco
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
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Hézode C, Hirschfield GM, Ghesquiere W, Sievert W, Rodriguez-Torres M, Shafran SD, Thuluvath PJ, Tatum HA, Waked I, Esmat G, Lawitz EJ, Rustgi VK, Pol S, Weis N, Pockros PJ, Bourlière M, Serfaty L, Vierling JM, Fried MW, Weiland O, Brunetto MR, Everson GT, Zeuzem S, Kwo PY, Sulkowski M, Bräu N, Hernandez D, McPhee F, Wind-Rotolo M, Liu Z, Noviello S, Hughes EA, Yin PD, Schnittman S. Daclatasvir plus peginterferon alfa and ribavirin for treatment-naive chronic hepatitis C genotype 1 or 4 infection: a randomised study. Gut 2015; 64:948-56. [PMID: 25080450 DOI: 10.1136/gutjnl-2014-307498] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/01/2014] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To evaluate the safety and efficacy of daclatasvir, an HCV NS5A inhibitor with pangenotypic activity, administered with peginterferon-alfa-2a/ribavirin. DESIGN In this Phase 2b double-blind, placebo-controlled study, treatment-naive adults with HCV genotype 1 (N=365) or 4 (N=30) infection were randomly assigned (2:2:1) to daclatasvir 20 mg or 60 mg, or placebo once daily plus weekly peginterferon-alfa-2a and twice-daily ribavirin. Daclatasvir recipients achieving protocol-defined response (PDR; HCV-RNA<lower limit of quantitation at Week 4 and undetectable at Week 10) were rerandomised at Week 12 to continue daclatasvir/peginterferon-alfa-2a/ribavirin for 24 weeks total duration or to placebo/peginterferon-alfa-2a/ribavirin for another 12 weeks. Patients without PDR and placebo patients continued peginterferon-alfa/ribavirin through Week 48. Primary efficacy endpoints were undetectable HCV-RNA at Weeks 4 and 12 (extended rapid virologic response, eRVR) and at 24 weeks post-treatment (sustained virologic response, SVR24) among genotype 1-infected patients. RESULTS Overall, eRVR was achieved by 54.4% (80/147) of genotype 1-infected patients receiving daclatasvir 20 mg, 54.1% (79/146) receiving 60 mg versus 13.9% (10/72) receiving placebo. SVR24 was achieved among 87 (59.2%), 87 (59.6%), and 27 (37.5%) patients in these groups, respectively. Higher proportions of genotype 4-infected patients receiving daclatasvir 20 mg (66.7%; 8/12) or 60 mg (100.0%; 12/12) achieved SVR24 versus placebo (50.0%; 3/6). A majority of daclatasvir-treated patients achieved PDR and experienced less virologic failure and higher SVR24 rates with a shortened 24-week treatment duration. Adverse events occurred with similar frequency across all treatment groups. CONCLUSIONS The combination of daclatasvir/peginterferon-alfa/ribavirin was generally well tolerated and achieved higher SVR24 rates compared with placebo/peginterferon-alfa/ribavirin among patients infected with HCV genotype 1 or 4. TRIAL REGISTRATION NUMBER NCT01125189.
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Affiliation(s)
- Christophe Hézode
- Hôpital Henri Mondor, AP-HP, Université Paris-Est, Inserm U955, Créteil, France
| | - Gideon M Hirschfield
- Centre for Liver Research and NIHR Biomedical Research Unit, University of Birmingham, Birmingham, UK
| | - Wayne Ghesquiere
- Vancouver Island Health Authority & University of British Columbia, Victoria, British Columbia, Canada
| | | | | | | | | | | | - Imam Waked
- National Liver Institute, Shebin Elkom, Egypt
| | - Gamal Esmat
- Endemic Medicine and Hepatogastroenterology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Eric J Lawitz
- Texas Liver Institute, University of Texas Health Science Center, San Antonio, Texas, USA
| | | | - Stanislas Pol
- Inserm U1016 and Liver Unit, Université Paris Descartes, Hôpital Cochin, Paris, France
| | - Nina Weis
- Copenhagen University Hospital, Hvidovre, Denmark
| | | | | | | | | | - Michael W Fried
- University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ola Weiland
- Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | | | | | | | - Paul Y Kwo
- Indiana University, Indianapolis, Indiana, USA
| | | | - Norbert Bräu
- James J. Peters VA Medical Center, Bronx, New York, USA
| | - Dennis Hernandez
- Bristol-Myers Squibb, Clinical Research and Development, Wallingford, Connecticut, USA
| | - Fiona McPhee
- Bristol-Myers Squibb, Clinical Research and Development, Wallingford, Connecticut, USA
| | - Megan Wind-Rotolo
- Bristol-Myers Squibb, Research and Development, Princeton, New Jersey, USA
| | - Zhaohui Liu
- Bristol-Myers Squibb Research and Development, Hopewell, New Jersey, USA
| | - Stephanie Noviello
- Bristol-Myers Squibb, Research and Development, Princeton, New Jersey, USA
| | - Eric A Hughes
- Bristol-Myers Squibb, Research and Development, Princeton, New Jersey, USA
| | - Philip D Yin
- Bristol-Myers Squibb, Clinical Research and Development, Wallingford, Connecticut, USA
| | - Steven Schnittman
- Bristol-Myers Squibb, Clinical Research and Development, Wallingford, Connecticut, USA
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Janardhan SV, Reau NS. Should NS5A inhibitors serve as the scaffold for all-oral anti-HCV combination therapies? ACTA ACUST UNITED AC 2015; 7:11-20. [PMID: 25926761 PMCID: PMC4403691 DOI: 10.2147/hmer.s79584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chronic hepatitis C virus (HCV) infection represents a global health problem that affects up to 130–150 million people worldwide. The HCV treatment landscape has been transformed recently by the introduction of direct-acting antiviral (DAA) agents that target viral proteins, including the NS3 protease, the NS5B polymerase, and the NS5A protein. Treatment with multiple DAAs in combination has been shown to result in high rates of sustained virologic response, without the need for pegylated interferon, and a shorter duration of therapy compared with interferon-based regimens; however, the optimal combination of DAAs has yet to be determined. The class of NS5A inhibitors has picomolar potency with pangenotypic activity, and recent clinical studies have shown these inhibitors to be an important component of DAA combination regimens. This review discusses the rational design of an optimal anti-HCV DAA cocktail, with a focus on the role of NS5A in the HCV life cycle, the attributes of the NS5A class of inhibitors, and the potential for NS5A inhibitors to act as a scaffold for DAA-only treatment regimens.
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Affiliation(s)
- Sujit V Janardhan
- Center for Liver Diseases, Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Nancy S Reau
- Center for Liver Diseases, Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
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Abstract
The carbamate group is a key structural motif in many approved drugs and prodrugs. There is an increasing use of carbamates in medicinal chemistry and many derivatives are specifically designed to make drug-target interactions through their carbamate moiety. In this Perspective, we present properties and stabilities of carbamates, reagents and chemical methodologies for the synthesis of carbamates, and recent applications of carbamates in drug design and medicinal chemistry.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Margherita Brindisi
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
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Kwon HJ, Xing W, Chan K, Niedziela-Majka A, Brendza KM, Kirschberg T, Kato D, Link JO, Cheng G, Liu X, Sakowicz R. Direct binding of ledipasvir to HCV NS5A: mechanism of resistance to an HCV antiviral agent. PLoS One 2015; 10:e0122844. [PMID: 25856426 PMCID: PMC4391872 DOI: 10.1371/journal.pone.0122844] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/19/2015] [Indexed: 01/01/2023] Open
Abstract
Ledipasvir, a direct acting antiviral agent (DAA) targeting the Hepatitis C Virus NS5A protein, exhibits picomolar activity in replicon cells. While its mechanism of action is unclear, mutations that confer resistance to ledipasvir in HCV replicon cells are located in NS5A, suggesting that NS5A is the direct target of ledipasvir. To date co-precipitation and cross-linking experiments in replicon or NS5A transfected cells have not conclusively shown a direct, specific interaction between NS5A and ledipasvir. Using recombinant, full length NS5A, we show that ledipasvir binds directly, with high affinity and specificity, to NS5A. Ledipasvir binding to recombinant NS5A is saturable with a dissociation constant in the low nanomolar range. A mutant form of NS5A (Y93H) that confers resistance to ledipasvir shows diminished binding to ledipasvir. The current study shows that ledipasvir inhibits NS5A through direct binding and that resistance to ledipasvir is the result of a reduction in binding affinity to NS5A mutants.
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Affiliation(s)
- Hyock Joo Kwon
- Gilead Sciences, Inc., Foster City, California, United States of America
- * E-mail:
| | - Weimei Xing
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Katie Chan
- Gilead Sciences, Inc., Foster City, California, United States of America
| | | | | | | | - Darryl Kato
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - John O. Link
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Guofeng Cheng
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Xiaohong Liu
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Roman Sakowicz
- Gilead Sciences, Inc., Foster City, California, United States of America
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Lindström I, Kjellin M, Palanisamy N, Bondeson K, Wesslén L, Lannergard A, Lennerstrand J. Prevalence of polymorphisms with significant resistance to NS5A inhibitors in treatment-naive patients with hepatitis C virus genotypes 1a and 3a in Sweden. Infect Dis (Lond) 2015; 47:555-62. [PMID: 25851241 DOI: 10.3109/23744235.2015.1028097] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The future treatment of hepatitis C virus (HCV) infection will be combinations of direct-acting antivirals (DAAs) that not only target multiple viral targets, but are also effective against different HCV genotypes. Of the many drug targets in HCV, one promising target is the non-structural 5A protein (NS5A), against which inhibitors, namely daclatasvir, ledipasvir and ombitasvir, have shown potent efficacy. However, since HCV is known to have very high sequence diversity, development of resistance is a problem against but not limited to NS5A inhibitors (i.e. resistance also found against NS3-protease and NS5B non-nucleoside inhibitors), when used in suboptimal combinations. Furthermore, it has been shown that natural resistance against DAAs is present in treatment-naïve patients and such baseline resistance will potentially complicate future treatment strategies. METHODS A pan-genotypic population-sequencing method with degenerated primers targeting the NS5A region was developed. We have investigated the prevalence of baseline resistant variants in 127 treatment-naïve patients of HCV genotypes 1a, 1b, 2b and 3a. RESULTS The method could successfully sequence more than 95% of genotype 1a, 1b and 3a samples. Interpretation of fold resistance data against the NS5A inhibitors was done with the help of earlier published phenotypic data. Baseline resistance variants associated with high resistance (1000-50,000-fold) was found in three patients: Q30H or Y93N in genotype 1a patients and further Y93H in a genotype 3a patient. CONCLUSION Using this method, baseline resistance can be examined and the data could have a potential role in selecting the optimal and cost-efficient treatment for the patient.
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Affiliation(s)
- Ida Lindström
- From the 1 Clinical Virology, Department of Medical Sciences, Uppsala University , Uppsala
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Fast hepatitis C virus RNA elimination and NS5A redistribution by NS5A inhibitors studied by a multiplex assay approach. Antimicrob Agents Chemother 2015; 59:3482-92. [PMID: 25845863 DOI: 10.1128/aac.00223-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/27/2015] [Indexed: 12/18/2022] Open
Abstract
While earlier therapeutic strategies for the treatment of hepatitis C virus (HCV) infection relied exclusively on interferon (IFN) and ribavirin (RBV), four direct-acting antiviral agents (DAAs) have now been approved, aiming for an interferon-free strategy with a short treatment duration and fewer side effects. To facilitate studies on the mechanism of action (MOA) and efficacy of DAAs, we established a multiplex assay approach, which employs flow cytometry, a Gaussia luciferase reporter system, Western blot analysis, reverse transcription-quantitative PCR (RT-qPCR), a limited dilution assay (50% tissue culture infectious dose [TCID50]), and an image profiling assay that follows the NS5A redistribution in response to drug treatment. We used this approach to compare the relative potency of various DAAs and the kinetics of their antiviral effects as a potential preclinical measure of their potential clinical utility. We evaluated the NS5A inhibitors ledipasvir (LDV) and daclatasvir (DCV), the NS3/4A inhibitor danoprevir (DNV), and the NS5B inhibitor sofosbuvir (SOF). In terms of kinetics, our data demonstrate that the NS5A inhibitor LDV, followed closely by DCV, has the fastest effect on suppression of viral proteins and RNA and on redistribution of NS5A. In terms of MOA, LDV has a more pronounced effect than DCV on the viral replication, assembly, and infectivity of released virus. Our approach can be used to facilitate the study of the biological processes involved in HCV replication and help identify optimal drug combinations.
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Zhong M, Peng E, Huang N, Huang Q, Huq A, Lau M, Colonno R, Li L. Potent bisimidazole-based HCV NS5A inhibitors bearing annulated tricyclic motifs. Bioorg Med Chem Lett 2014; 24:5738-5742. [DOI: 10.1016/j.bmcl.2014.10.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/11/2014] [Accepted: 10/17/2014] [Indexed: 01/09/2023]
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Berger C, Romero-Brey I, Radujkovic D, Terreux R, Zayas M, Paul D, Harak C, Hoppe S, Gao M, Penin F, Lohmann V, Bartenschlager R. Daclatasvir-like inhibitors of NS5A block early biogenesis of hepatitis C virus-induced membranous replication factories, independent of RNA replication. Gastroenterology 2014; 147:1094-105.e25. [PMID: 25046163 DOI: 10.1053/j.gastro.2014.07.019] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 06/21/2014] [Accepted: 07/15/2014] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS Direct-acting antivirals that target nonstructural protein 5A (NS5A), such as daclatasvir, have high potency against the hepatitis C virus (HCV). They are promising clinical candidates, yet little is known about their antiviral mechanisms. We investigated the mechanisms of daclatasvir derivatives. METHODS We used a combination of biochemical assays, in silico docking models, and high-resolution imaging to investigate inhibitor-induced changes in properties of NS5A, including its interaction with phosphatidylinositol-4 kinase IIIα and induction of the membranous web, which is the site of HCV replication. Analyses were conducted with replicons, infectious virus, and human hepatoma cells that express a HCV polyprotein. Studies included a set of daclatasvir derivatives and HCV variants with the NS5A inhibitor class-defining resistance mutation Y93H. RESULTS NS5A inhibitors did not affect NS5A stability or dimerization. A daclatasvir derivative interacted with NS5A and molecular docking studies revealed a plausible mode by which the inhibitor bound to NS5A dimers. This interaction was impaired in mutant forms of NS5A that are resistant to daclatavir, providing a possible explanation for the reduced sensitivity of the HCV variants to this drug. Potent NS5A inhibitors were found to block HCV replication by preventing formation of the membranous web, which was not linked to an inhibition of phosphatidylinositol-4 kinase IIIα. Correlative light-electron microscopy revealed unequivocally that NS5A inhibitors had no overall effect on the subcellular distribution of NS5A, but completely prevented biogenesis of the membranous web. CONCLUSIONS Highly potent inhibitors of NS5A, such as daclatasvir, block replication of HCV RNA at the stage of membranous web biogenesis-a new paradigm in antiviral therapy.
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Affiliation(s)
- Carola Berger
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Inés Romero-Brey
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Danijela Radujkovic
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Raphael Terreux
- CNRS, UMR5086, Bases Moléculaires et Structurales des Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, Lyon, France; Labex Ecofect (ANR-11-LABX-0042), University of Lyon, Lyon, France; Faculté de Pharmacie (ISPB), Lyon, France
| | - Margarita Zayas
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - David Paul
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Christian Harak
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Simone Hoppe
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Min Gao
- Bristol-Myers Squibb Research and Development, Wallingford, Connecticut
| | - Francois Penin
- CNRS, UMR5086, Bases Moléculaires et Structurales des Systèmes Infectieux, Institut de Biologie et Chimie des Protéines, Lyon, France; Labex Ecofect (ANR-11-LABX-0042), University of Lyon, Lyon, France
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Centre for Infection Research, Heidelberg University, Heidelberg, Germany.
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Eyre NS, Helbig KJ, Beard MR. Current and future targets of antiviral therapy in the hepatitis C virus life cycle. Future Virol 2014. [DOI: 10.2217/fvl.14.83] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT Advances in our understanding of the hepatitis C virus (HCV) life cycle have enabled the development of numerous clinically advanced direct-acting antivirals. Indeed, the recent approval of first-generation direct-acting antivirals that target the viral NS3–4A protease and NS5B RNA-dependent RNA polymerase brings closer the possibility of universally efficacious and well-tolerated antiviral therapies for this insidious infection. However, the complexities of comorbidities, unforeseen side effects or drug–drug interactions, viral diversity, the high mutation rate of HCV RNA replication and the elegant and constantly evolving mechanisms employed by HCV to evade host and therapeutically implemented antiviral strategies remain as significant obstacles to this goal. Here, we review advances in our understanding of the HCV life cycle and associated opportunities for antiviral therapy.
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Affiliation(s)
- Nicholas S Eyre
- School of Molecular & Biomedical Science, The University of Adelaide & Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Karla J Helbig
- School of Molecular & Biomedical Science, The University of Adelaide & Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Michael R Beard
- School of Molecular & Biomedical Science, The University of Adelaide & Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
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Eyre NS, Beard MR. HCV NS5A inhibitors disrupt replication factory formation: a novel mechanism of antiviral action. Gastroenterology 2014; 147:959-62. [PMID: 25265576 DOI: 10.1053/j.gastro.2014.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Nicholas S Eyre
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia; Centre for Cancer Biology, Adelaide, Australia
| | - Michael R Beard
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia; Centre for Cancer Biology, Adelaide, Australia.
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Zhong M, Peng E, Huang N, Huang Q, Huq A, Lau M, Colonno R, Li L. Discovery of functionalized bisimidazoles bearing cyclic aliphatic-phenyl motifs as HCV NS5A inhibitors. Bioorg Med Chem Lett 2014; 24:5731-5737. [PMID: 25453810 DOI: 10.1016/j.bmcl.2014.10.057] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/11/2014] [Accepted: 10/17/2014] [Indexed: 02/06/2023]
Abstract
This Letter describes the discovery of a number of functionalized bisimidazoles bearing a cyclohexylphenyl, piperidylphenyl, or bicyclo[2,2,2]octylphenyl motif as HCV NS5A inhibitors. Compounds 2c, 4b and 6 have demonstrated low single-digit nM potency in gt-1a replicon and double-digit pM potency in gt-1b replicon, respectively. Moreover, both 4b and 6 have, respectively, exhibited good oral bioavailability in rats with a favorable liver/plasma ratio of the drug concentration.
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Affiliation(s)
- Min Zhong
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA.
| | - Eric Peng
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Ningwu Huang
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Qi Huang
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Anja Huq
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Meiyen Lau
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Richard Colonno
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA
| | - Leping Li
- Presidio Pharmaceuticals, Inc., 1700 Owens Street, Suite 585, San Francisco, CA 94158, USA.
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McCormick AL, Moynihan L, Macartney MJ, Garcia-Diaz A, Smith C, Johnson MA, Rodger AJ, Bhagani S, Haque T, Webster DP. Baseline drug resistance mutations are detectable in HCV genes NS3 and NS5A but not NS5B in acute and chronic HIV-coinfected patients. Antivir Ther 2014; 20:361-3. [PMID: 25279548 DOI: 10.3851/imp2871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Adele L McCormick
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK.
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Lim PJ, Gallay PA. Hepatitis C NS5A protein: two drug targets within the same protein with different mechanisms of resistance. Curr Opin Virol 2014; 8:30-7. [PMID: 24879295 PMCID: PMC4195798 DOI: 10.1016/j.coviro.2014.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 12/18/2022]
Abstract
The era of interferon-free antiviral treatments for hepatitis C virus infection has arrived. With increasing numbers of approved antivirals, evaluating all parameters that may influence response is necessary to choose optimal combinations for treatment success. Targeting NS5A has become integral in antiviral combinations in clinical development. Daclatasvir and ledipasvir belong to the NS5A inhibitor class, which directly target the NS5A protein. Alisporivir, a host-targeting antiviral, is a cyclophilin inhibitor that indirectly targets NS5A by blocking NS5A/cyclophilin A interaction. Resistance to daclatasvir and ledipasvir differs from alisporivir, with mutations arising in NS5A domains I and II, respectively. Combining these two classes acting on distinct NS5A domains represents an attractive strategy for potentially effective interferon-free treatments for chronic hepatitis C infection.
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Affiliation(s)
- Precious J Lim
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Philippe A Gallay
- Department of Immunology & Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
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NS5A inhibitors impair NS5A-phosphatidylinositol 4-kinase IIIα complex formation and cause a decrease of phosphatidylinositol 4-phosphate and cholesterol levels in hepatitis C virus-associated membranes. Antimicrob Agents Chemother 2014; 58:7128-40. [PMID: 25224012 DOI: 10.1128/aac.03293-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The hepatitis C virus (HCV) nonstructural (NS) protein 5A is a multifunctional protein that plays a central role in viral replication and assembly. Antiviral agents directly targeting NS5A are currently in clinical development. Although the elucidation of the mechanism of action (MOA) of NS5A inhibitors has been the focus of intensive research, a detailed understanding of how these agents exert their antiviral effect is still lacking. In this study, we observed that the downregulation of NS5A hyperphosphorylation is associated with the actions of NS5A inhibitors belonging to different chemotypes. NS5A is known to recruit the lipid kinase phosphatidylinositol 4-kinase IIIα (PI4KIIIα) to the HCV-induced membranous web in order to generate phosphatidylinositol 4-phosphate (PI4P) at the sites of replication. We demonstrate that treatment with NS5A inhibitors leads to an impairment in the NS5A-PI4KIIIα complex formation that is paralleled by a significant reduction in PI4P and cholesterol levels within the endomembrane structures of HCV-replicating cells. A similar decrease in PI4P and cholesterol levels was also obtained upon treatment with a PI4KIIIα-targeting inhibitor. In addition, both the NS5A and PI4KIIIα classes of inhibitors induced similar subcellular relocalization of the NS5A protein, causing the formation of large cytoplasmic NS5A-containing clusters previously reported to be one of the hallmarks of inhibition of the action of PI4KIIIα. Because of the similarities between the effects induced by treatment with PI4KIIIα or NS5A inhibitors and the observation that agents targeting NS5A impair NS5A-PI4KIIIα complex formation, we speculate that NS5A inhibitors act by interfering with the function of the NS5A-PI4KIIIα complex.
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Ivachtchenko AV, Mitkin OD, Yamanushkin PM, Kuznetsova IV, Bulanova EA, Shevkun NA, Koryakova AG, Karapetian RN, Bichko VV, Trifelenkov AS, Kravchenko DV, Vostokova NV, Veselov MS, Chufarova NV, Ivanenkov YA. Discovery of novel highly potent hepatitis C virus NS5A inhibitor (AV4025). J Med Chem 2014; 57:7716-30. [PMID: 25148100 DOI: 10.1021/jm500951r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A series of next in class small-molecule hepatitis C virus (HCV) NS5A inhibitors with picomolar potency containing 2-pyrrolidin-2-yl-5-{4-[4-(2-pyrrolidin-2-yl-1H-imidazol-5-yl)buta-1,3-diynyl]phenyl}-1H-imidazole cores was designed based on the SAR studies available for the reported NS5A inhibitors. Compound 13a (AV4025), with (S,S,S,S)-stereochemistry (EC50 = 3.4 ± 0.2 pM, HCV replicon genotype 1b), was dramatically more active than were the compounds with two (S)- and two (R)-chiral centers. Human serum did not significantly reduce the antiviral activity (<4-fold). Relatively favorable pharmacokinetic features and good oral bioavailability were observed during animal studies. Compound 13a was well tolerated in rodents (in mice, LD50 = 2326 mg/kg or higher), providing a relatively high therapeutic index. During safety, pharmacology and subchronic toxicity studies in rats and dogs, it was not associated with any significant pathological or clinical findings. This compound is currently being evaluated in phase I/II clinical trials for the treatment of HCV infection.
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Affiliation(s)
- Alexandre V Ivachtchenko
- Alla Chem LLC , 1835 East Hallandale Beach Boulevard 442, Hallandale Beach, Florida 33009, United States
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A randomized, double-blind, multiple-dose study of the pan-genotypic NS5A inhibitor samatasvir in patients infected with hepatitis C virus genotype 1, 2, 3 or 4. J Hepatol 2014; 60:920-7. [PMID: 24434503 DOI: 10.1016/j.jhep.2014.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/29/2013] [Accepted: 01/06/2014] [Indexed: 01/02/2023]
Abstract
BACKGROUND & AIMS Samatasvir is a pan-genotypic inhibitor of the hepatitis C (HCV) non-structural protein 5A (NS5A). This study evaluated the antiviral activity, pharmacokinetics and safety of samatasvir monotherapy in treatment-naïve subjects infected with HCV genotype 1-4. METHODS Thirty-four genotype 1 and thirty genotype 2, 3 or 4 subjects were randomized to receive for 3days placebo or samatasvir 25-100mg per day. Plasma samples for HCV RNA, pharmacokinetics and sequencing were collected up to day 10. RESULTS Samatasvir achieved potent antiviral activity across genotypes: mean maximum reductions from baseline were 3.2-3.6 (genotype 1a), 3.0-4.3 (genotype 1b), 3.2-3.4 (genotype 3), and 3.6-3.9 (genotype 4) log10/ml respectively; no viral rebound was observed during the 3-day treatment period. For genotype 2 HCV, samatasvir was active in subjects with NS5A L31 polymorphism at baseline (individual range 2.5-4.1 log10/ml), but showed minimal activity in those with baseline M31 polymorphism. Samatasvir exhibited a long plasma half-life of approximately 20h which supports once daily dosing. Samatasvir was well tolerated in all subjects with no safety-related discontinuations or serious adverse events. The most common adverse events included constipation, nausea and headache and occurred at similar frequency in active and placebo subjects. All events were mild or moderate in intensity. There were no patterns or dose dependence of adverse events, vital signs, laboratory parameters or electrocardiograms. CONCLUSIONS Samatasvir 25-100mg monotherapy for 3days was well tolerated and induced a rapid and profound reduction in plasma HCV RNA in subjects infected with HCV genotype 1-4. Samatasvir is being evaluated in combination with other direct-acting antiviral agents in subjects with HCV infection.
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Ascher DB, Wielens J, Nero TL, Doughty L, Morton CJ, Parker MW. Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA. Sci Rep 2014; 4:4765. [PMID: 24755925 PMCID: PMC3996483 DOI: 10.1038/srep04765] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 04/07/2014] [Indexed: 12/23/2022] Open
Abstract
Hepatitis C virus (HCV) infection affects more than 170 million people. The high genetic variability of HCV and the rapid development of drug-resistant strains are driving the urgent search for new direct-acting antiviral agents. A new class of agents has recently been developed that are believed to target the HCV protein NS5A although precisely where they interact and how they affect function is unknown. Here we describe an in vitro assay based on microscale thermophoresis and demonstrate that two clinically relevant inhibitors bind tightly to NS5A domain 1 and inhibit RNA binding. Conversely, RNA binding inhibits compound binding. The compounds bind more weakly to known resistance mutants L31V and Y93H. The compounds do not affect NS5A dimerisation. We propose that current NS5A inhibitors act by favouring a dimeric structure of NS5A that does not bind RNA.
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Affiliation(s)
- David B. Ascher
- ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3056, Australia
| | - Jerome Wielens
- ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3056, Australia
- Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia
| | - Tracy L. Nero
- ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3056, Australia
| | - Larissa Doughty
- ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3056, Australia
| | - Craig J. Morton
- ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3056, Australia
| | - Michael W. Parker
- ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3056, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
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Barakat KH, Anwar-Mohamed A, Tuszynski JA, Robins MJ, Tyrrell DL, Houghton M. A Refined Model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes. J Chem Inf Model 2014; 55:362-73. [PMID: 24730573 DOI: 10.1021/ci400631n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many direct-acting antiviral agents (DAAs) that selectively block hepatitis C virus (HCV) replication are currently under development. Among these agents is Daclatasvir, a first-in-class inhibitor targeting the NS5A viral protein. Although Daclatasvir is the most potent HCV antiviral molecule yet developed, its binding location and mode of binding remain unknown. The drug exhibits a low barrier to resistance mutations, particularly in genotype 1 viruses, but its efficacy against other genotypes is unclear. Using state-of-the-art modeling techniques combined with the massive computational power of Blue Gene/Q, we identified the atomic interactions of Daclatasvir within NS5A for different HCV genotypes and for several reported resistant mutations. The proposed model is the first to reveal the detailed binding mode of Daclatasvir. It also provides a tool to facilitate design of second generation drugs, which may confer less resistance and/or broader activity against HCV.
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Affiliation(s)
- Khaled H Barakat
- Li Ka Shing Institute of Virology, University of Alberta , Edmonton, Alberta Canada
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