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Mousa MHA, Ahmed NS, Schwedtmann K, Frakolaki E, Vassilaki N, Zoidis G, Weigand JJ, Abadi AH. Design and Synthesis of Novel Symmetric Fluorene-2,7-Diamine Derivatives as Potent Hepatitis C Virus Inhibitors. Pharmaceuticals (Basel) 2021; 14:ph14040292. [PMID: 33806139 PMCID: PMC8064491 DOI: 10.3390/ph14040292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus (HCV) is an international challenge. Since the discovery of NS5A direct-acting antivirals, researchers turned their attention to pursue novel NS5A inhibitors with optimized design and structure. Herein we explore highly potent hepatitis C virus (HCV) NS5A inhibitors; the novel analogs share a common symmetrical prolinamide 2,7-diaminofluorene scaffold. Modification of the 2,7-diaminofluorene backbone included the use of (S)-prolinamide or its isostere (S,R)-piperidine-3-caboxamide, both bearing different amino acid residues with terminal carbamate groups. Compound 26 exhibited potent inhibitory activity against HCV genotype (GT) 1b (effective concentration (EC50) = 36 pM and a selectivity index of >2.78 × 106). Compound 26 showed high selectivity on GT 1b versus GT 4a. Interestingly, it showed a significant antiviral effect against GT 3a (EC50 = 1.2 nM). The structure-activity relationship (SAR) analysis revealed that picomolar inhibitory activity was attained with the use of S-prolinamide capped with R- isoleucine or R-phenylglycine residues bearing a terminal alkyl carbamate group.
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Affiliation(s)
- Mai H. A. Mousa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Nermin S. Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
- Correspondence: (N.S.A.); (A.H.A.); Tel.: +202-27590700 (ext. 3429) (N.S.A.); +202-27590700 (ext. 3400) (A.H.A.); Fax: +202-27581041 (N.S.A. & A.H.A.)
| | - Kai Schwedtmann
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany; (K.S.); (J.J.W.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, 11521 Athens, Greece; (E.F.); (N.V.)
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Jan J. Weigand
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany; (K.S.); (J.J.W.)
| | - Ashraf H. Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
- Correspondence: (N.S.A.); (A.H.A.); Tel.: +202-27590700 (ext. 3429) (N.S.A.); +202-27590700 (ext. 3400) (A.H.A.); Fax: +202-27581041 (N.S.A. & A.H.A.)
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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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Lee SH, Moon JS, Pak BY, Kim GW, Lee W, Cho H, Kim S, Kim SJ, Oh JW. HA1077 displays synergistic activity with daclatasvir against hepatitis C virus and suppresses the emergence of NS5A resistance-associated substitutions in mice. Sci Rep 2018; 8:12469. [PMID: 30127498 PMCID: PMC6102265 DOI: 10.1038/s41598-018-30460-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/31/2018] [Indexed: 02/08/2023] Open
Abstract
The kinase C-related kinase 2 (PRK2), which phosphorylates hepatitis C virus (HCV) RNA polymerase, is a proviral factor enhancing HCV replication. Here, we report on the in vivo anti-HCV efficacy of HA1077, which inhibits viral genome replication by targeting PRK2 and displays viral entry inhibitory activity by targeting Rho-associated kinase. HA1077 showed synergistic antiviral activity selectively with nonstructural protein 5 A (NS5A) inhibitors including daclatasvir (DCV). HA1077 oral administration substantially reduced serum viral loads in mice bearing HCV genotype 2a-replicating Huh7 xenografts. When administered with DCV, HA1077 potentiated the antiviral efficacy of DCV and suppressed the generation of DCV resistance-associated variants (RAVs). By deep-sequencing analysis, we uncovered an unprecedented DCV-induced polymorphism at the poly-proline motif (PxxPxxP) of NS5A. Coadministration of HA1077 reduced such a polymorphism. Overall, our results demonstrate the potential therapeutic benefit of combination therapy with HA1077 plus DCV for HCV patients carrying emerging or pre-existing RAVs toward NS5A inhibitors.
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Affiliation(s)
- Seung-Hoon Lee
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Jae-Su Moon
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Bo-Yeong Pak
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Geon-Woo Kim
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Wooseong Lee
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Hee Cho
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - SangKyu Kim
- Department of Systems Immunology, Gangwon National University, Gangwon-do, 24341, Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea.
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Beldar S, Manimekalai MSS, Cho NJ, Baek K, Grüber G, Yoon HS. Self-association and conformational variation of NS5A domain 1 of hepatitis C virus. J Gen Virol 2018; 99:194-208. [PMID: 29300159 DOI: 10.1099/jgv.0.001000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Direct-acting antivirals (DAAs) targeting the non-structural 5A (NS5A) protein of the hepatitis C virus (HCV) are crucial drugs that have shown exceptional clinical success in patients. However, their mode of action (MoA) remains unclear, and drug-resistant HCV strains are rapidly emerging. It is critical to characterize the behaviour of the NS5A protein in solution, which can facilitate the development of new classes of inhibitors or improve the efficacy of the currently available DAAs. Using biophysical methods, including dynamic light scattering, size exclusion chromatography and chemical cross-linking experiments, we showed that the NS5A domain 1 from genotypes 1b and 1a of the HCV intrinsically self-associated and existed as a heterogeneous mixture in solution. Interestingly, the NS5A domain 1 from genotypes 1b and 1a exhibited different dynamic equilibria of monomers to higher-order structures. Using small-angle X-ray scattering, we studied the structural dynamics of the various states of the NS5A domain 1 in solution. We also tested the effect of daclatasvir (DCV), the most prominent DAA, on self-association of the wild and DCV-resistant mutant (Y93H) NS5A domain 1 proteins, and demonstrated that DCV induced the formation of large and irreversible protein aggregates that eventually precipitated out. This study highlights the conformational variability of the NS5A domain 1 of HCV, which may be an intrinsic structural behaviour of the HCV NS5A domain 1 in solution.
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Affiliation(s)
- Serap Beldar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Kwanghee Baek
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ho Sup Yoon
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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Ivanenkov YA, Aladinskiy VA, Bushkov NA, Ayginin AA, Majouga AG, Ivachtchenko AV. Small-molecule inhibitors of hepatitis C virus (HCV) non-structural protein 5A (NS5A): a patent review (2010-2015). Expert Opin Ther Pat 2017; 27:401-414. [PMID: 27967269 DOI: 10.1080/13543776.2017.1272573] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Non-structural 5A (NS5A) protein has achieved a considerable attention as an attractive target for the treatment of hepatitis C (HCV). A number of novel NS5A inhibitors have been reported to date. Several drugs having favorable ADME properties and mild side effects were launched into the pharmaceutical market. For instance, daclatasvir was launched in 2014, elbasvir is currently undergoing registration, ledipasvir was launched in 2014 as a fixed-dose combination with sofosbuvir (NS5B inhibitor). Areas covered: Thomson integrity database and SciFinder database were used as a valuable source to collect the patents on small-molecule NS5A inhibitors. All the structures were ranked by the date of priority. Patent holder and antiviral activity for each scaffold claimed were summarized and presented in a convenient manner. A particular focus was placed on the best-in-class bis-pyrrolidine-containing NS5A inhibitors. Expert opinion: Several first generation NS5A inhibitors have recently progressed into advanced clinical trials and showed superior efficacy in reducing viral load in infected subjects. Therapy schemes of using these agents in combination with other established antiviral drugs with complementary mechanisms of action can address the emergence of resistance and poor therapeutic outcome frequently attributed to antiviral drugs.
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Affiliation(s)
- Yan A Ivanenkov
- a Department of Biological and Medical Physics , Moscow Institute of Physics and Technology (State University) , Dolgoprudny City , Moscow Region , Russia.,b Department of Computational and Medicinal Chemistry , ChemDiv , San Diego , CA , USA.,c Chemistry Department , Moscow State University , Moscow , Russia
| | - Vladimir A Aladinskiy
- a Department of Biological and Medical Physics , Moscow Institute of Physics and Technology (State University) , Dolgoprudny City , Moscow Region , Russia
| | - Nikolay A Bushkov
- a Department of Biological and Medical Physics , Moscow Institute of Physics and Technology (State University) , Dolgoprudny City , Moscow Region , Russia
| | - Andrey A Ayginin
- a Department of Biological and Medical Physics , Moscow Institute of Physics and Technology (State University) , Dolgoprudny City , Moscow Region , Russia
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Ahmed M, Pal A, Houghton M, Barakat K. A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry. ACS Infect Dis 2016; 2:872-881. [PMID: 27933783 DOI: 10.1021/acsinfecdis.6b00113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Direct-acting antivirals (DAAs) form the current standard of care (SOC) against hepatitis C virus (HCV). These drugs selectively target the viral proteins, offering a unique mechanism to avoid toxicity, to increase their efficacy, and to evolve from decades of interferon- and ribavirin-based therapy. Among the promising HCV targets for DAAs is the NS5A protein, and daclatasvir (DCV) forms a first-in-class compound that selectively targets this protein. Despite the exceptional potency of DCV (∼picomolar IC50) and although several DCV derivatives have been approved for human use or are close to approval, the exact mode of action of these drugs is still incomplete. This is simply due to the vast complexity of cocrystallizing DCV with NS5A in the absence of two amphipathic helices that are required for DCV binding. In this context, computational modeling provides a unique alternative to solve this problem. Here, we build upon our recent discovery of a completely symmetrical interaction between DCV and NS5A and investigate the mode of binding of six other structures similar to DCV. The selected compounds include both symmetric and asymmetric molecules. In addition, we show that our model correlates very well with mutations that can confer resistance to DCV. The current study enhances our understanding of the mode of action of this class of HCV inhibitors and helps in defining the origin of resistance to these drugs.
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Affiliation(s)
- Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
| | - Abhishek Pal
- Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - Michael Houghton
- Li Ka Shing Institute of Virology, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
- Li Ka Shing Applied Virology Institute, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
- Li Ka Shing Institute of Virology, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
- Li Ka Shing Applied Virology Institute, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
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