1
|
Hussain A. DEAD Box RNA Helicases: Biochemical Properties, Role in RNA Processing and Ribosome Biogenesis. Cell Biochem Biophys 2024:10.1007/s12013-024-01240-w. [PMID: 38430409 DOI: 10.1007/s12013-024-01240-w] [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: 12/12/2022] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
DEAD box RNA helicases are a versatile group of ATP dependent enzymes that play an essential role in cellular processes like transcription, RNA processing, ribosome biogenesis and translation. These enzymes perform structural rearrangement of complex RNA molecules and enhance the productive folding of RNA and organization of macromolecular complexes. In this review article besides providing the outline about structural organization of helicases, an in-depth discussion will be done on the biochemical properties of RNA helicases like their substrate binding, binding and hydrolysis of ATP and related conformational changes that are important for functioning of the RNA helicase enzymes. I will extensively discuss the physiological role of RNA helicases in RNA processing and ribosome biogenesis.
Collapse
Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
| |
Collapse
|
2
|
Qian X, Qi Z. Mosquito-Borne Flaviviruses and Current Therapeutic Advances. Viruses 2022; 14:v14061226. [PMID: 35746697 PMCID: PMC9229039 DOI: 10.3390/v14061226] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 12/10/2022] Open
Abstract
Mosquito-borne flavivirus infections affect approximately 400 million people worldwide each year and are global threats to public health. The common diseases caused by such flaviviruses include West Nile, yellow fever, dengue, Zika infection and Japanese encephalitis, which may result in severe symptoms and disorders of multiple organs or even fatal outcomes. Till now, no specific antiviral agents are commercially available for the treatment of the diseases. Numerous strategies have been adopted to develop novel and promising inhibitors against mosquito-borne flaviviruses, including drugs targeting the critical viral components or essential host factors during infection. Research advances in antiflaviviral therapy might optimize and widen the treatment options for flavivirus infection. This review summarizes the current developmental progresses and involved molecular mechanisms of antiviral agents against mosquito-borne flaviviruses.
Collapse
|
3
|
Du Pont KE, McCullagh M, Geiss BJ. Conserved motifs in the flavivirus NS3 RNA helicase enzyme. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1688. [PMID: 34472205 PMCID: PMC8888775 DOI: 10.1002/wrna.1688] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Flaviviruses are a major health concern because over half of the world population is at risk of infection and there are very few antiviral therapeutics to treat diseases resulting from infection. Replication is an essential part of the flavivirus survival. One of the viral proteins, NS3 helicase, is critical for unwinding the double stranded RNA intermediate during flaviviral replication. The helicase performs the unwinding of the viral RNA intermediate structure in an ATP-dependent manner. NS3 helicase is a member of the Viral/DEAH-like subfamily of the superfamily 2 helicase containing eight highly conserved structural motifs (I, Ia, II, III, IV, IVa, V, and VI) localized between the ATP-binding and RNA-binding pockets. Of these structural motifs only three are well characterized for function in flaviviruses (I, II, and VI). The roles of the other structural motifs are not well understood for NS3 helicase function, but comparison of NS3 with other superfamily 2 helicases within the viral/DEAH-like, DEAH/RHA, and DEAD-box subfamilies can be used to elucidate the roles of these structural motifs in the flavivirus NS3 helicase. This review aims to summarize the role of each conserved structural motif within flavivirus NS3 in RNA helicase function. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Kelly E. Du Pont
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA,School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
El-Tahan RR, Ghoneim AM, Zaghloul H. Dissection of two drug-targeted regions of Hepatitis C virus subtype 4a infecting Egyptian patients. Virus Genes 2020; 56:564-581. [PMID: 32572756 PMCID: PMC7307947 DOI: 10.1007/s11262-020-01776-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Recently, treatment of HCV infection has been improved after the development of direct acting antivirals (DAAs) which target different viral proteins (NS3-4A, NS5A and NS5B). The activity and effectiveness of these DAAs are affected by the presence of resistance associated substitutions (RASs). This study aimed to characterize HCV genotypes circulating among Egyptian HCV patients, to dissect the full sequences of HCV NS3-4A and NS5B regions, and to characterize RASs associated with NS3-4A and NS5B inhibitors in HCV treatment-naïve patients. Genotyping of 80 HCV samples from treatment-naïve patients was done using restriction fragment length polymorphism and phylogenetic analysis based on some full NS5B sequences. Results showed the prevalence of HCV subtype 4a. Twenty four new full sequences of NS3-4A and NS5B regions of subtype 4a were deposited in the GenBank database. In general, the substitutions associated with NS3-4A-targeting drugs were absent predicting possible responsiveness of Egyptian HCV patients to these drugs. In addition, the absence of amino acid substitutions associated with resistance to Sofosbuvir may predict good response to treatment with Sofosbuvir. Some amino acid substitutions associated with resistance to different classes of non-nucleoside inhibitors were detected. Further investigations on treated Egyptian HCV patients may evaluate the effectiveness of the massively used drugs. Many predicted T-cell-binding epitopes in NS3-4A and NS5B regions were found to be highly conserved in the currently studied isolates; a finding that might be important for HCV vaccine development. We demonstrated potential NS3 epitopes that could be used in engineering T cells against HCV epitopes.
Collapse
Affiliation(s)
- Radwa R El-Tahan
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt
| | - Ahmed M Ghoneim
- Zoology Department, Faculty of Science, Damietta University, New Damietta, P.O. 34517, Damietta, Egypt.
| | - Hosam Zaghloul
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| |
Collapse
|
6
|
Chou YC. Mechanical mechanism for the translocation of hexameric and nonstructural helicases: Dependence on physical parameters. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:21. [PMID: 32303848 DOI: 10.1140/epje/i2020-11944-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
Three recently observed facts of the translocation of actual hexameric and nonstructural (NS) helicases are related to the various physical quantities and are in accordance with the recently proposed mechanical mechanism: a) the translocation of hexameric helicases might be led by either the N-terminal domain (NTD) or C-terminal domain (CTD) depending on which domain has a smaller central pore, b) the translocation speed (vt) of the ring-shaped helicases and NS helicases decreased with decreasing applied tension, and c) a large difference in the vt of the NS helicase was observed for the helicase translocating on DNA and RNA. These findings are the effects of the physical quantities of the helicase/nuclei acid strands on the translocation of helicases and are difficult to explain with biochemical models. We predict that a similar behavior as described in b) and c) is also shown by hexameric helicases. The validity of the mechanical mechanism is demonstrated in simulation experiments.
Collapse
Affiliation(s)
- Y C Chou
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan.
| |
Collapse
|
7
|
Fathima Rizwana B, Prasana JC, Muthu S, Abraham CS. Vibrational spectroscopy, reactive site analysis and molecular docking studies on 2-[(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)methoxy]-3-hydroxypropyl (2S)-2-amino-3-methylbutanoate. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Gao Y, Yang W. Different mechanisms for translocation by monomeric and hexameric helicases. Curr Opin Struct Biol 2019; 61:25-32. [PMID: 31783299 DOI: 10.1016/j.sbi.2019.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 11/24/2022]
Abstract
Helicases are ATP-dependent motor proteins that translocate along single-stranded or double-stranded nucleic acids to alter base-pairing structures or molecular interactions. Helicases can be divided to monomeric and hexameric types, each with distinct ternary structures, nucleic acid-binding modes, and translocation mechanisms. It is well established that monomeric helicases translocate by the inchworm mechanism. Recent structures of different superfamilies of hexameric helicases reveal that they use a hand-over hand mechanism for translocation. Structures of bacteriophage T7 replisome illustrate how helicase and polymerase cooperatively catalyze DNA unwinding. In this review, we survey structures of monomeric and hexameric helicases and compare different mechanisms for translocation.
Collapse
Affiliation(s)
- Yang Gao
- Department of Biosciences, Rice University, Houston, TX 77030, USA.
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
9
|
Togashi Y, Flechsig H. Coarse-Grained Protein Dynamics Studies Using Elastic Network Models. Int J Mol Sci 2018; 19:ijms19123899. [PMID: 30563146 PMCID: PMC6320916 DOI: 10.3390/ijms19123899] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/28/2018] [Accepted: 12/03/2018] [Indexed: 01/03/2023] Open
Abstract
Elastic networks have been used as simple models of proteins to study their slow structural dynamics. They consist of point-like particles connected by linear Hookean springs and hence are convenient for linear normal mode analysis around a given reference structure. Furthermore, dynamic simulations using these models can provide new insights. As the computational cost associated with these models is considerably lower compared to that of all-atom models, they are also convenient for comparative studies between multiple protein structures. In this review, we introduce examples of coarse-grained molecular dynamics studies using elastic network models and their derivatives, focusing on the nonlinear phenomena, and discuss their applicability to large-scale macromolecular assemblies.
Collapse
Affiliation(s)
- Yuichi Togashi
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
- RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
- Cybermedia Center, Osaka University, 5-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| |
Collapse
|
10
|
Rizwana B. F, Muthu S, Prasana JC, Abraham CS, Raja M. Spectroscopic (FT-IR, FT-Raman) investigation, topology (ESP, ELF, LOL) analyses, charge transfer excitation and molecular docking (dengue, HCV) studies on ribavirin. ACTA ACUST UNITED AC 2018. [PMCID: PMC7148669 DOI: 10.1016/j.cdc.2018.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Fathima Rizwana B.
- Department of Physics, Madras Christian College, Chennai 600059 Tamil Nadu, India
| | - S. Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar 604407 Tamil Nadu, India
- Corresponding author.
| | | | | | - M. Raja
- Department of Physics, Government Thirumagal Mills College, Vellore 635803 Tamil Nadu, India
| |
Collapse
|
11
|
Yerukhimovich MM, Marohnic CC, Frick DN. Role of the Conserved DECH-Box Cysteine in Coupling Hepatitis C Virus Helicase-Catalyzed ATP Hydrolysis to RNA Unwinding. Biochemistry 2018; 57:6247-6255. [PMID: 30281972 DOI: 10.1021/acs.biochem.8b00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DECH-box proteins are a subset of DExH/D-box superfamily 2 helicases possessing a conserved Asp-Glu-Cys-His motif in their ATP binding site. The conserved His helps position the Asp and Glu residues, which coordinate the divalent metal cation that connects the protein to ATP and activate the water molecule needed for ATP hydrolysis, but the role of the Cys is still unclear. This study uses site-directed mutants of the model DECH-box helicase encoded by the hepatitis C virus (HCV) to examine the role of the Cys in helicase action. Proteins lacking a Cys unwound DNA less efficiently than wild-type proteins did. For example, at low protein concentrations, a helicase harboring a Gly instead of the DECH-box Cys unwound DNA more slowly than the wild-type helicase did, but at higher protein concentrations, the two proteins unwound DNA at similar rates. All HCV proteins analyzed had similar affinities for ATP and nucleic acids and hydrolyzed ATP in the presence of RNA at similar rates. However, in the absence of RNA, all proteins lacking a DECH-box cysteine hydrolyzed ATP 10-15 times faster with higher Km values, and lower apparent affinities for metal ions, compared to those observed with wild-type proteins. These differences were observed with proteins isolated from HCV genotypes 2a and 1b, suggesting that this role is conserved. These data suggest the helicase needs Cys292 to bind ATP in a state where ATP is not hydrolyzed until RNA binds.
Collapse
Affiliation(s)
- Mark M Yerukhimovich
- Department of Chemistry & Biochemistry , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
| | - Christopher C Marohnic
- Abbott Laboratories , 100 Abbott Park Road , Abbott Park , Illinois 60064 , United States
| | - David N Frick
- Department of Chemistry & Biochemistry , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
| |
Collapse
|
12
|
Bansal R, Arya V, Sethy R, Rakesh R, Muthuswami R. RecA-like domain 2 of DNA-dependent ATPase A domain, a SWI2/SNF2 protein, mediates conformational integrity and ATP hydrolysis. Biosci Rep 2018; 38:BSR20180568. [PMID: 29748240 PMCID: PMC6019379 DOI: 10.1042/bsr20180568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/27/2022] Open
Abstract
ATP-dependent chromatin remodeling proteins use the energy released from ATP hydrolysis to reposition nucleosomes in DNA-dependent processes. These proteins are classified as SF2 helicases. SMARCAL1, a member of this protein family, is known to modulate both DNA repair and transcription by specifically recognizing DNA molecules possessing double-strand to single-strand transition regions. Mutations in this gene cause a rare autosomal recessive disorder known as Schimke Immuno-Osseous Dysplasia (SIOD).Structural studies have shown that the ATP-dependent chromatin remodeling proteins possess two RecA-like domains termed as RecA-like domain 1 and RecA-like domain 2. Using Active DNA-dependent ATPase A domain (ADAAD), the bovine homolog of SMARCAL1, as a model system we had previously shown that the RecA-like domain 1 containing helicase motifs Q, I, Ia, II, and III are sufficient for ligand binding; however, the Rec A-like domain 2 containing motifs IV, V, and VI are needed for ATP hydrolysis. In the present study, we have focused on the motifs present in the RecA-like domain 2. Our studies demonstrate that the presence of an aromatic residue in motif IV is needed for interaction with DNA in the presence of ATP. We also show that the motif V is required for the catalytic efficiency of the protein and motif VI is needed for interaction with DNA in the presence of ATP. Finally, we show that the SIOD-associated mutation, R820H, present in motif VI results in loss of ATPase activity, and therefore, reduced response to DNA damage.
Collapse
Affiliation(s)
- Ritu Bansal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vijendra Arya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ramesh Sethy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Rohini Muthuswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
13
|
Asselah T, Hassanein T, Waked I, Mansouri A, Dusheiko G, Gane E. Eliminating hepatitis C within low-income countries - The need to cure genotypes 4, 5, 6. J Hepatol 2018; 68:814-826. [PMID: 29229584 DOI: 10.1016/j.jhep.2017.11.037] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/01/2017] [Accepted: 11/13/2017] [Indexed: 12/19/2022]
Abstract
Around 70 to 100 million people are chronically infected with HCV worldwide. HCV antiviral drug development has revolutionised the treatment of HCV, with several direct-acting antiviral agents offering patients the chance of cure after only 8-12 weeks of treatment. Drug development was initially focussed on HCV genotype 1 (GT1) infection, since this was the most prevalent worldwide, although clinical trials included all genotypes prevalent in the US and Europe. Because the earliest in vitro assays utilised the GT1b and 2 replicons, the initial classes of direct-acting antivirals (protease inhibitors, non-nucleotide polymerase inhibitors) were GT1-specific, albeit they had an effect on other less prevalent genotypes. Epidemiological data has shown the regional importance of other HCV genotypes. More than 50% of all HCV infections around the globe are not with GT1. The prevalence of HCV genotype 4 (GT4), 5 (GT5), and 6 (GT6) is increasing in North America and Europe due to migration from the Middle East, Africa and South-East Asia. With the successful development of the multi and pan-genotypic non-structural protein 5A inhibitors, second generation protease inhibitors and nucleotide non-structural protein 5B inhibitors comes a unique opportunity to achieve global HCV elimination. The goal of this review is to summarise the available information pertaining to GT4, GT5 and GT6, with a specific focus on direct-acting antiviral agents.
Collapse
Affiliation(s)
- Tarik Asselah
- Centre de Recherche sur l'Inflammation, Viral Hepatitis INSERM UMR 1149, Université Paris Diderot, Department of Hepatology, AP-HP Hôpital Beaujon, Clichy, France.
| | - Tarek Hassanein
- Southern California GI and Liver Centers and Southern California Research Center, Coronado, CA, USA
| | - Imam Waked
- National Liver Institute, Menoufiya, Egypt
| | - Abdellah Mansouri
- Centre de Recherche sur l'Inflammation, Viral Hepatitis INSERM UMR 1149, Université Paris Diderot, Department of Hepatology, AP-HP Hôpital Beaujon, Clichy, France
| | - Geoffrey Dusheiko
- UCL Institute of Liver and Digestive Health, University College London Medical School, Kings College Hospital, London, UK
| | - Edward Gane
- Liver Unit, Auckland City Hospital, Auckland, New Zealand
| |
Collapse
|
14
|
Eyer L, Nencka R, de Clercq E, Seley-Radtke K, Růžek D. Nucleoside analogs as a rich source of antiviral agents active against arthropod-borne flaviviruses. Antivir Chem Chemother 2018; 26:2040206618761299. [PMID: 29534608 PMCID: PMC5890575 DOI: 10.1177/2040206618761299] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/30/2018] [Indexed: 12/27/2022] Open
Abstract
Nucleoside analogs represent the largest class of small molecule-based antivirals, which currently form the backbone of chemotherapy of chronic infections caused by HIV, hepatitis B or C viruses, and herpes viruses. High antiviral potency and favorable pharmacokinetics parameters make some nucleoside analogs suitable also for the treatment of acute infections caused by other medically important RNA and DNA viruses. This review summarizes available information on antiviral research of nucleoside analogs against arthropod-borne members of the genus Flavivirus within the family Flaviviridae, being primarily focused on description of nucleoside inhibitors of flaviviral RNA-dependent RNA polymerase, methyltransferase, and helicase/NTPase. Inhibitors of intracellular nucleoside synthesis and newly discovered nucleoside derivatives with high antiflavivirus potency, whose modes of action are currently not completely understood, have drawn attention. Moreover, this review highlights important challenges and complications in nucleoside analog development and suggests possible strategies to overcome these limitations.
Collapse
Affiliation(s)
- Luděk Eyer
- Department of Virology, Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Erik de Clercq
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Daniel Růžek
- Department of Virology, Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| |
Collapse
|
15
|
Lin CT, Tritschler F, Lee KS, Gu M, Rice CM, Ha T. Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase. Protein Sci 2017; 26:1391-1403. [PMID: 28176403 DOI: 10.1002/pro.3136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 01/23/2023]
Abstract
Non-structural protein 3 (NS3) is an essential enzyme and a therapeutic target of hepatitis C virus (HCV). Compared to NS3-catalyzed nucleic acids unwinding, its translation on single stranded nucleic acids have received relatively little attention. To investigate the NS3h translocation with single-stranded nucleic acids substrates directly, we have applied a hybrid platform of single-molecule fluorescence detection combined with optical trapping. With the aid of mechanical manipulation and fluorescence localization, we probed the translocase activity of NS3h on laterally stretched, kilobase-size single-stranded DNA and RNA. We observed that the translocation rate of NS3h on ssDNA at a rate of 24.4 nucleotides per second, and NS3h translocates about three time faster on ssRNA, 74 nucleotides per second. The translocation speed was minimally affected by the applied force. A subpopulation of NS3h underwent a novel translocation mode on ssDNA where the stretched DNA shortened gradually and then recovers its original length abruptly before repeating the cycle repetitively. The speed of this mode of translocation was reduced with increasing force. With corroborating data from single-molecule fluorescence resonance energy transfer (smFRET) experiments, we proposed that NS3h can cause repetitive looping of DNA. The smFRET dwell time analysis showed similar translocation time between sole translocation mode versus repetitive looping mode, suggesting that the motor domain exhibits indistinguishable enzymatic activities between the two translocation modes. We propose a potential secondary nucleic acids binding site at NS3h which might function as an anchor point for translocation-coupled looping.
Collapse
Affiliation(s)
- Chang-Ting Lin
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Felix Tritschler
- Department of Physics Education, Kongju National University, Kongju, 32588, Republic of Korea.,Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | - Kyung Suk Lee
- Department of Physics Education, Kongju National University, Kongju, 32588, Republic of Korea
| | - Meigang Gu
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York
| | - Charles M Rice
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland.,Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland.,Howard Hughes Medical Institute, Baltimore, Maryland
| |
Collapse
|
16
|
Ablenas CJ, Liu HW, Shkriabai N, Kvaratskhelia M, Cosa G, Götte M. Dynamic Interconversions of HCV Helicase Binding Modes on the Nucleic Acid Substrate. ACS Infect Dis 2017; 3:99-109. [PMID: 28081608 DOI: 10.1021/acsinfecdis.6b00177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The dynamics involved in the interaction between hepatitis C virus nonstructural protein 3 (NS3) C-terminal helicase and its nucleic acid substrate have been the subject of interest for some time given the key role of this enzyme in viral replication. Here, we employed fluorescence-based techniques and focused on events that precede the unwinding process. Both ensemble Förster resonance energy transfer (FRET) and ensemble protein induced fluorescence enhancement (PIFE) assays show binding on the 3' single-stranded overhang of model DNA substrates (>5 nucleotides) with no preference for the single-stranded/double-stranded (ss/ds) junction. Single-molecule PIFE experiments revealed three enhancement levels that correspond to three discrete binding sites at adjacent bases. The enzyme is able to transition between binding sites in both directions without dissociating from the nucleic acid. In contrast, the NS3 mutant W501A, which is unable to engage in stacking interactions with the DNA, is severely compromised in this switching activity. Altogether our data are consistent with a model for NS3 dynamics that favors ATP-independent random binding and sliding by one and two nucleotides along the overhang of the loading strand.
Collapse
Affiliation(s)
| | - Hsiao-Wei Liu
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gonzalo Cosa
- Department of Chemistry and the Centre for Self-Assembled Chemical
Structures (CSACS/CRMAA), McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Matthias Götte
- Department
of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| |
Collapse
|
17
|
Abstract
Approximately 170 million people are chronically infected with HCV and 350 million are chronically infected with HBV worldwide. It is estimated that more than one million patients die from complications related to chronic viral hepatitis, mainly HCC which is one of the most frequent cancers in many countries, especially Africa, the Middle East and Asia. HCV drug development has been impressive, and this revolution led to several direct-acting antiviral agents achieving an HCV cure after only 6-12 weeks. This progress could theorically lead to HCV global elimination making HCV and its consequences a rarity. HBV research and development programs can learn from the HCV experience, to achieve an HBV functional or sterilizing cure. This review will summarize key steps which have been realized for an HCV cure, and discuss the next steps to achieve for an HCV elimination. And also, how this HCV revolution has inspired scientists and clinicians to achieve the same for HBV.
Collapse
Affiliation(s)
- Raymond F Schinazi
- Frances Winship Walters Professor of Pediatrics, Center for AIDS Research, Emory University School of Medicine, Atlanta, GA, USA
| | - Tarik Asselah
- Hepatology Department, UMR1149, Physiopathology and Treatment of Viral Hepatitis, Centre de Recherche sur l'Inflammation and Université Denis Diderot Paris 7, Beaujon Hospital, AP-HP, Clichy, France
| |
Collapse
|
18
|
Abstract
The need for antiviral drugs is growing rapidly as more viral diseases are recognized. The methods used to discover these drugs have evolved considerably over the past 40 years and the overall process of discovery can be broken down into sub-processes which include lead generation, lead optimization and lead development. Various methods are now employed to ensure these processes are carried out efficiently. For lead generation, screening methodologies have developed to the extent where hundreds of thousands of compounds can be screened against a particular target. An alternative approach is to use the structures of enzyme substrates as a starting point for drug discovery. Much use is now made of X-ray crystallographic data of target–inhibitor complexes for the optimization of lead structures, and methods for preparing libraries of compounds to assist both generation and optimization of leads are welldeveloped. The methods used to predict and improve the pharmacokinetic properties of compounds are also changing rapidly. Finally, novel approaches to antiviral therapy using oligonucleotide-based compounds or modulating the host immune response are also being explored. This review discusses these approaches, provides examples of where their application has been successful and sets them against a historical background.
Collapse
Affiliation(s)
- PS Jones
- Roche Discovery Welwyn, 40 Broadwater Road, Welwyn Garden City, AL7 3AY, UK
| |
Collapse
|
19
|
Provazzi PJS, Mukherjee S, Hanson AM, Nogueira ML, Carneiro BM, Frick DN, Rahal P. Analysis of the Enzymatic Activity of an NS3 Helicase Genotype 3a Variant Sequence Obtained from a Relapse Patient. PLoS One 2015; 10:e0144638. [PMID: 26658750 PMCID: PMC4684341 DOI: 10.1371/journal.pone.0144638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 11/20/2015] [Indexed: 12/15/2022] Open
Abstract
The hepatitis C virus (HCV) is a species of diverse genotypes that infect over 170 million people worldwide, causing chronic inflammation, cirrhosis and hepatocellular carcinoma. HCV genotype 3a is common in Brazil, and it is associated with a relatively poor response to current direct-acting antiviral therapies. The HCV NS3 protein cleaves part of the HCV polyprotein, and cellular antiviral proteins. It is therefore the target of several HCV drugs. In addition to its protease activity, NS3 is also an RNA helicase. Previously, HCV present in a relapse patient was found to harbor a mutation known to be lethal to HCV genotype 1b. The point mutation encodes the amino acid substitution W501R in the helicase RNA binding site. To examine how the W501R substitution affects NS3 helicase activity in a genotype 3a background, wild type and W501R genotype 3a NS3 alleles were sub-cloned, expressed in E. coli, and the recombinant proteins were purified and characterized. The impact of the W501R allele on genotype 2a and 3a subgenomic replicons was also analyzed. Assays monitoring helicase-catalyzed DNA and RNA unwinding revealed that the catalytic efficiency of wild type genotype 3a NS3 helicase was more than 600 times greater than the W501R protein. Other assays revealed that the W501R protein bound DNA less than 2 times weaker than wild type, and both proteins hydrolyzed ATP at similar rates. In Huh7.5 cells, both genotype 2a and 3a subgenomic HCV replicons harboring the W501R allele showed a severe defect in replication. Since the W501R allele is carried as a minor variant, its replication would therefore need to be attributed to the trans-complementation by other wild type quasispecies.
Collapse
Affiliation(s)
- Paola J. S. Provazzi
- São Paulo State University - UNESP, Department of Biology, São José do Rio Preto/SP, CEP: 15054–000, Brazil
- * E-mail:
| | - Sourav Mukherjee
- University of Wisconsin- Milwaukee, Department of Chemistry & Biochemistry, Milwaukee, WI, 53217, United States of America
| | - Alicia M. Hanson
- University of Wisconsin- Milwaukee, Department of Chemistry & Biochemistry, Milwaukee, WI, 53217, United States of America
| | - Mauricio L. Nogueira
- São José do Rio Preto Medical School, Laboratory of Virology, São José do Rio Preto/SP, CEP: 15090–000, Brazil
| | - Bruno M. Carneiro
- São Paulo State University - UNESP, Department of Biology, São José do Rio Preto/SP, CEP: 15054–000, Brazil
| | - David N. Frick
- University of Wisconsin- Milwaukee, Department of Chemistry & Biochemistry, Milwaukee, WI, 53217, United States of America
| | - Paula Rahal
- São Paulo State University - UNESP, Department of Biology, São José do Rio Preto/SP, CEP: 15054–000, Brazil
| |
Collapse
|
20
|
Kumar GS, Basu A. The use of calorimetry in the biophysical characterization of small molecule alkaloids binding to RNA structures. Biochim Biophys Acta Gen Subj 2015; 1860:930-944. [PMID: 26522497 DOI: 10.1016/j.bbagen.2015.10.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/06/2015] [Accepted: 10/27/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND RNA has now emerged as a potential target for therapeutic intervention. RNA targeted drug design requires detailed thermodynamic characterization that provides new insights into the interactions and this together with structural data, may be used in rational drug design. The use of calorimetry to characterize small molecule-RNA interactions has emerged as a reliable and sensitive tool after the recent advancements in biocalorimetry. SCOPE OF THE REVIEW This review summarizes the recent advancements in thermodynamic characterization of small molecules, particularly some natural alkaloids binding to various RNA structures. Thermodynamic characterization provides information that can supplement structural data leading to more effective drug development protocols. MAJOR CONCLUSIONS This review provides a concise report on the use of isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) techniques in characterizing small molecules, mostly alkaloids-RNA interactions with particular reference to binding of tRNA, single stranded RNA, double stranded RNA, poly(A), triplex RNA. GENERAL SIGNIFICANCE It is now apparent that a combination of structural and thermodynamic data is essential for rational design of specific RNA targeted drugs. Recent advancements in biocalorimetry instrumentation have led to detailed understanding of the thermodynamics of small molecules binding to various RNA structures paving the path for the development of many new natural and synthetic molecules as specific binders to various RNA structures. RNA targeted drug design, that remained unexplored, will immensely benefit from the calorimetric studies leading to the development of effective drugs for many diseases.
Collapse
Affiliation(s)
- Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| | - Anirban Basu
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| |
Collapse
|
21
|
Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases. Proc Natl Acad Sci U S A 2015; 112:4292-7. [PMID: 25831501 DOI: 10.1073/pnas.1416746112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. Here, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3' single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ∼90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. This bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.
Collapse
|
22
|
X-ray structure of the pestivirus NS3 helicase and its conformation in solution. J Virol 2015; 89:4356-71. [PMID: 25653438 DOI: 10.1128/jvi.03165-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
UNLABELLED Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of nonstructural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at a 2.5-Å resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, as it contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses from which the core protein is deleted map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with the findings of small-angle X-ray-scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a nonhydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. IMPORTANCE Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the nonstructural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the unwinding specificity of pNS3h, which is active only on RNA duplexes. We also show that pNS3h has a highly dynamic behavior--a characteristic probably shared with NS3 helicases from all Flaviviridae members--that could be targeted for drug design by using recent algorithms to specifically block molecular motion. Compounds that lock the enzyme in a single conformation or limit its dynamic range of conformations are indeed likely to block its helicase function.
Collapse
|
23
|
Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases. Int J Mol Sci 2015; 16:2269-93. [PMID: 25622248 PMCID: PMC4346836 DOI: 10.3390/ijms16022269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 12/28/2022] Open
Abstract
The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.
Collapse
|
24
|
Asselah T, Marcellin P. Optimal IFN-free therapy in treatment-naïve patients with HCV genotype 1 infection. Liver Int 2015; 35 Suppl 1:56-64. [PMID: 25529088 DOI: 10.1111/liv.12745] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There has been a revolution in the treatment of chronic hepatitis C. Several oral regimens combining direct-acting antivirals (DAAs) from different families [NS5B nucleotide inhibitors, NS5B non-nucleoside inhibitors, NS5A replication complex inhibitors and NS3/4A protease inhibitors (PI)] are under development. These regimens result in an increase in sustained virological response (SVR) rates to above 90% and reduce the duration of treatment to twelve weeks or less. As of 2015 several regimens will be approved with additive potencies, without cross-resistance and with a good safety profile. Remaining issues will include increasing screening and access to care so that HCV may become the first chronic viral infection eradicated worldwide. This review summarizes results obtained with oral DAAs combinations, that have been approved and/or have completed phase III clinical trials for HCV genotype 1 (HCV-1) treatment-naïve patients.
Collapse
Affiliation(s)
- Tarik Asselah
- Hepatology Department, AP-HP, CRB3, Beaujon Hospital, University Paris Diderot 7 and INSERM U773, Clichy, France
| | | |
Collapse
|
25
|
Ventura GT, da Costa ECB, Capaccia AM, Mohana-Borges R. pH-dependent conformational changes in the HCV NS3 protein modulate its ATPase and helicase activities. PLoS One 2014; 9:e115941. [PMID: 25551442 PMCID: PMC4281115 DOI: 10.1371/journal.pone.0115941] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/29/2014] [Indexed: 11/29/2022] Open
Abstract
The hepatitis C virus (HCV) infects 170 to 200 million people worldwide and is, therefore, a major health problem. The lack of efficient treatments that specifically target the viral proteins or RNA and its high chronicity rate make hepatitis C the cause of many deaths and hepatic transplants annually. The NS3 protein is considered an important target for the development of anti-HCV drugs because it is composed of two domains (a serine protease in the N-terminal portion and an RNA helicase/NTPase in the C-terminal portion), which are essential for viral replication and proliferation. We expressed and purified both the NS3 helicase domain (NS3hel) and the full-length NS3 protein (NS3FL) and characterized pH-dependent structural changes associated with the increase in their ATPase and helicase activities at acidic pH. Using intrinsic fluorescence experiments, we have observed that NS3hel was less stable at pH 6.4 than at pH 7.2. Moreover, binding curves using an extrinsic fluorescent probe (bis-ANS) and ATPase assays performed under different pH conditions demonstrated that the hydrophobic clefts of NS3 are significantly more exposed to the aqueous medium at acidic pH. Using fluorescence spectroscopy and anisotropy assays, we have also observed more protein interaction with DNA upon pH acidification, which suggests that the hydrophobic clefts exposure on NS3 might be related to a loss of stability that could lead it to adopt a more open conformation. This conformational change at acidic pH would stimulate both its ATPase and helicase activities, as well as its ability to bind DNA. Taken together, our results indicate that the NS3 protein adopts a more open conformation due to acidification from pH 7.2 to 6.4, resulting in a more active form at a pH that is found near Golgi-derived membranes. This increased activity could better allow NS3 to carry out its functions during HCV replication.
Collapse
Affiliation(s)
- Gustavo Tavares Ventura
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Emmerson Corrêa Brasil da Costa
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Anne Miranda Capaccia
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ronaldo Mohana-Borges
- Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- * E-mail:
| |
Collapse
|
26
|
Comparison of structural architecture of HCV NS3 genotype 1 versus Pakistani genotype 3a. BIOMED RESEARCH INTERNATIONAL 2014; 2014:749254. [PMID: 25401105 PMCID: PMC4221965 DOI: 10.1155/2014/749254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 08/10/2014] [Accepted: 08/19/2014] [Indexed: 11/17/2022]
Abstract
This study described the structural characterization of Pakistani HCV NS3 GT3a in parallel with genotypes 1a and 1b NS3. We investigated the role of amino acids and their interaction patterns in different HCV genotypes by crystallographic modeling. Different softwares were used to study the interaction pattern, for example, CLCBIO sequence viewer, MODELLER, NMRCLUST, ERRAT score, and MODELLER. Sixty models were produced and clustered into groups and the best model of PK-NCVI/Pk3a NS3 was selected and studied further to check the variability with other HCV NS3 genotypes. This study will help in future to understand the structural architecture of HCV genome variability and to further define the conserved targets for antiviral agents.
Collapse
|
27
|
Nonstructural protein 5A (NS5A) and human replication protein A increase the processivity of hepatitis C virus NS5B polymerase activity in vitro. J Virol 2014; 89:165-80. [PMID: 25320291 DOI: 10.1128/jvi.01677-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED The precise role(s) and topological organization of different factors in the hepatitis C virus (HCV) RNA replication complex are not well understood. In order to elucidate the role of viral and host proteins in HCV replication, we have developed a novel in vitro replication system that utilizes a rolling-circle RNA template. Under close-to-physiological salt conditions, HCV NS5BΔ21, an RNA-dependent RNA polymerase, has poor affinity for the RNA template. Human replication protein A (RPA) and HCV NS5A recruit NS5BΔ21 to the template. Subsequently, NS3 is recruited to the replication complex by NS5BΔ21, resulting in RNA synthesis stimulation by helicase. Both RPA and NS5A(S25-C447), but not NS5A(S25-K215), enabled the NS5BΔ21-NS3 helicase complex to be stably associated with the template and synthesize RNA product in a highly processive manner in vitro. This new in vitro HCV replication system is a useful tool that may facilitate the study of other replication factors and aid in the discovery of novel inhibitors of HCV replication. IMPORTANCE The molecular mechanism of hepatitis C virus (HCV) replication is not fully understood, but viral and host proteins collaborate in this process. Using a rolling-circle RNA template, we have reconstituted an in vitro HCV replication system that allows us to interrogate the role of viral and host proteins in HCV replication and delineate the molecular interactions. We showed that HCV NS5A(S25-C447) and cellular replication protein A (RPA) functionally cooperate as a processivity factor to stimulate HCV replication by HCV NS5BΔ21 polymerase and NS3 helicase. This system paves the way to test other proteins and may be used as an assay for discovery of HCV inhibitors.
Collapse
|
28
|
Docking studies of Pakistani HCV NS3 helicase: a possible antiviral drug target. PLoS One 2014; 9:e106339. [PMID: 25188400 PMCID: PMC4154687 DOI: 10.1371/journal.pone.0106339] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 07/19/2014] [Indexed: 01/02/2023] Open
Abstract
The nonstructural protein 3 (NS3) of hepatitis C virus (HCV) helicase is believed to be essential for viral replication and has become an attractive target for the development of antiviral drugs. The study of helicase is useful for elucidating its involvement in positive sense single-stranded RNA virus replication and to serve as templates for the design of novel antiviral drugs. In recent years, several models have been proposed on the conformational change leading to protein movement and RNA unwinding. Some compounds have been recently reported to inhibit the helicase and these include small molecules, RNA aptamers and antibodies. The current study is designed to help gain insights for the consideration of potential inhibitors for Pakistani HCV NS3 helicase protein. We have cloned, expressed and purified HCV NS3 helicase from Pakistani HCV serum samples and determined its 3D structure and employed it further in computational docking analysis to identify inhibitors against HCV genotype 3a (GT3a),including six antiviral key molecules such as quercetin, beta-carotene, resveratrol, catechins, lycopene and lutein. The conformation obtained after docking showed good hydrogen bond (HBond) interactions with best docking energy for quercetin and catechins followed by resveratrol and lutein. These anti-helicase key molecules will offer an alternative attraction to target the viral helicase, due to the current limitation with the interferon resistance treatment and presences of high rate of resistance in anti-protease inhibitor classes.
Collapse
|
29
|
Fan X, Xue B, Dolan PT, LaCount DJ, Kurgan L, Uversky VN. The intrinsic disorder status of the human hepatitis C virus proteome. MOLECULAR BIOSYSTEMS 2014; 10:1345-63. [PMID: 24752801 DOI: 10.1039/c4mb00027g] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many viral proteins or their biologically important regions are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions do not possess unique structures and possess functions that complement the functional repertoire of "normal" ordered proteins and domains, with many protein functional classes being heavily dependent on the intrinsic disorder. Viruses commonly use these highly flexible regions to invade the host organisms and to hijack various host systems. These disordered regions also help viruses in adapting to their hostile habitats and to manage their economic usage of genetic material. In this article, we focus on the structural peculiarities of proteins from human hepatitis C virus (HCV) and use a wide spectrum of bioinformatics techniques to evaluate the abundance of intrinsic disorder in the completed proteomes of several human HCV genotypes, to analyze the peculiarities of disorder distribution within the individual HCV proteins, and to establish potential roles of the structural disorder in functions of ten HCV proteins. We show that the intrinsic disorder or increased flexibility is not only abundant in these proteins, but is also absolutely necessary for their functions, playing a crucial role in the proteolytic processing of the HCV polyprotein, the maturation of the individual HCV proteins, and being related to the posttranslational modifications of these proteins and their interactions with DNA, RNA, and various host proteins.
Collapse
Affiliation(s)
- Xiao Fan
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta AB T6G 2V4, Canada.
| | | | | | | | | | | |
Collapse
|
30
|
Zheng W, Tekpinar M. Analysis of protein conformational transitions using elastic network model. Methods Mol Biol 2014; 1084:159-72. [PMID: 24061921 DOI: 10.1007/978-1-62703-658-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
In this chapter, we demonstrate the usage of a coarse-grained elastic network model to analyze protein conformational transitions in the NS3 helicase (NS3hel) of Hepatitis C virus (HCV). This analysis allows us to identify and visualize collective domain motions involved in the conformational transitions and predict the order of structural events during the transitions. It is highly efficient and applicable to many multi-domain protein structures which undergo large conformational changes to fulfill their functions. This method is made available through a Web server ( http://enm.lobos.nih.gov ).
Collapse
Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, NY, USA
| | | |
Collapse
|
31
|
Flechsig H. Computational biology approach to uncover hepatitis C virus helicase operation. World J Gastroenterol 2014; 20:3401-3409. [PMID: 24707123 PMCID: PMC3974507 DOI: 10.3748/wjg.v20.i13.3401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings.
Collapse
|
32
|
Guo M, Vidhyasagar V, Ding H, Wu Y. Insight into the roles of helicase motif Ia by characterizing Fanconi anemia group J protein (FANCJ) patient mutations. J Biol Chem 2014; 289:10551-10565. [PMID: 24573678 DOI: 10.1074/jbc.m113.538892] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding and remodeling of structured DNA or RNA, which is coordinated by conserved helicase motifs. FANCJ is a DNA helicase that is genetically linked to Fanconi anemia, breast cancer, and ovarian cancer. Here, we characterized two Fanconi anemia patient mutations, R251C and Q255H, that are localized in helicase motif Ia. Our genetic complementation analysis revealed that both the R251C and Q255H alleles failed to rescue cisplatin sensitivity of a FANCJ null cell line as detected by cell survival or γ-H2AX foci formation. Furthermore, our biochemical assays demonstrated that both purified recombinant proteins abolished DNA helicase activity and failed to disrupt the DNA-protein complex. Intriguingly, R251C impaired DNA binding ability to single-strand DNA and double-strand DNA, whereas Q255H retained higher binding activity to these DNA substrates compared with wild-type FANCJ protein. Consequently, R251C abolished its DNA-dependent ATP hydrolysis activity, whereas Q255H retained normal ATPase activity. Physically, R251C had reduced ATP binding ability, whereas Q255H had normal ATP binding ability and could translocate on single-strand DNA. Although both proteins were recruited to damage sites in our laser-activated confocal assays, they lost their DNA repair function, which explains why they exerted a domain negative effect when expressed in a wild-type background. Taken together, our work not only reveals the structural function of helicase motif Ia but also provides the molecular pathology of FANCJ in related diseases.
Collapse
Affiliation(s)
- Manhong Guo
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Venkatasubramanian Vidhyasagar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Hao Ding
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada.
| |
Collapse
|
33
|
Rosenquist Å, Samuelsson B, Johansson PO, Cummings MD, Lenz O, Raboisson P, Simmen K, Vendeville S, de Kock H, Nilsson M, Horvath A, Kalmeijer R, de la Rosa G, Beumont-Mauviel M. Discovery and Development of Simeprevir (TMC435), a HCV NS3/4A Protease Inhibitor. J Med Chem 2014; 57:1673-93. [DOI: 10.1021/jm401507s] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Maxwell D. Cummings
- Janssen Research & Development, LLC, Spring House, Pennsylvania 19002, United States
| | - Oliver Lenz
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Kenny Simmen
- Janssen Infectious Diseases BVBA, Beerse 2340, Belgium
| | | | - Herman de Kock
- Galapagos NV Generaal De Wittelaan, L11A3-2800, Mechelen, Belgium
| | | | | | | | - Guy de la Rosa
- Janssen Global Services, LLC, Titusville, New Jersey 08560, United States
| | | |
Collapse
|
34
|
Schinazi R, Halfon P, Marcellin P, Asselah T. HCV direct-acting antiviral agents: the best interferon-free combinations. Liver Int 2014; 34 Suppl 1:69-78. [PMID: 24373081 PMCID: PMC7737539 DOI: 10.1111/liv.12423] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For HCV infection, there have been major advancements during last several years with large numbers of ongoing trials with various direct-acting antivirals (DAA) showing high potency, favourable tolerability profile, higher barrier to resistance, shortened treatment duration, all oral regimen, pan-genotypic, fewer drug interactions and reduced pill burden. By 2014, several DAAs are anticipated to complete successful phase III trials and will be commercially available. Initially, a wave of IFN-based regimen (sofosbuvir, faldaprevir and simeprevir) will be available for treatment of HCV genotype 1. In the near future, combination of antiviral agents with additive potency that lack cross-resistance with good safety profile will likely be the new recommended regimens, making HCV, the first chronic viral infection to be eradicated worldwide with a finite duration of combination DAA therapy without IFN or ribavirin. The aim of this review was to summarize the results obtained from recent DAA combination studies without IFN.
Collapse
Affiliation(s)
- Raymond Schinazi
- Center for AIDS Research, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, GA, USA
| | - Philippe Halfon
- Internal Medicine and Infectious Diseases Department, Hôpital Europeen and Laboratoire Alphabio Marseille, Marseille, France
| | - Patrick Marcellin
- Hepatology Department, AP-HP, University Paris Diderot 7 and INSERM U773, CRB3, Beaujon Hospital, Clichy, France
| | - Tarik Asselah
- Hepatology Department, AP-HP, University Paris Diderot 7 and INSERM U773, CRB3, Beaujon Hospital, Clichy, France
| |
Collapse
|
35
|
LaPlante SR, Padyana AK, Abeywardane A, Bonneau P, Cartier M, Coulombe R, Jakalian A, Wildeson-Jones J, Li X, Liang S, McKercher G, White P, Zhang Q, Taylor SJ. Integrated Strategies for Identifying Leads That Target the NS3 Helicase of the Hepatitis C Virus. J Med Chem 2014; 57:2074-90. [DOI: 10.1021/jm401432c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Steven R. LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | | - Pierre Bonneau
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Mireille Cartier
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - René Coulombe
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Araz Jakalian
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | | | | - Ginette McKercher
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Peter White
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D, 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | | | | |
Collapse
|
36
|
Abstract
INTRODUCTION The current treatment for hepatitis C virus (HCV) genotype 1 chronic infection is the addition of direct-acting antivirals (DAAs) with a protease inhibitor (telaprevir or boceprevir) to the pegylated interferon (PEG-IFN) and ribavirin (RBV) regimen. In 2014, sofosbuvir, simeprevir and faldaprevir may be available, each in combination with PEG-IFN/RBV triple therapy. All the HCV enzymes are essential for HCV replication, and are potential drug discovery targets. Therefore, DAAs with different viral targets, including NS3 protease inhibitors, nucleoside/nucleotide analogue and nonnucleoside inhibitors of the RNA-dependent RNA polymerase, and NS5A replication complex inhibitors are under development. AREAS COVERED Interestingly, several IFN-free Phase III trials are ongoing with promising results. Among DAAs, sofosbuvir is a potent HCV-specific nucleotide analog (chain terminator). The aim of this article is to review sofosbuvir data, in particular Phase III trials. EXPERT OPINION Sofosbuvir has a high barrier to resistance with no virologic breakthrough to date. It has a pan-genotypic activity (even though lower rates of response for genotype 3). So far, no safety signal in preclinical/clinical studies has been observed with this compound. It is given orally, once daily, without food effect. Sofosbuvir will first be available in association with PEG-IFN/RBV. Sofosbuvir appears to be a key compound and a backbone for future IFN free treatment regimen.
Collapse
Affiliation(s)
- Tarik Asselah
- Université Paris Diderot-Paris 7, Assistance Publique-Hôpitaux de Paris, Hôpital Beaujon, Centre de Recherche Biomédicale Bichat-Beaujon CRB3, Service d'Hépatologie, Inserm Unité 773 , 100 Bd du Général Leclerc, 92110, Clichy and Paris , France +33 0 140875579 ; +33 0 147309440 ;
| |
Collapse
|
37
|
Ozen A, Sherman W, Schiffer CA. Improving the Resistance Profile of Hepatitis C NS3/4A Inhibitors: Dynamic Substrate Envelope Guided Design. J Chem Theory Comput 2013; 9:5693-5705. [PMID: 24587770 DOI: 10.1021/ct400603p] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Drug resistance is a principal concern in the treatment of quickly evolving diseases. The viral protease NS3/4A is a primary drug target for the hepatitis C virus (HCV) and is known to evolve resistance mutations in response to drug therapy. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition by NS3/4A; the drug resistant protease variants are no longer effectively inhibited by the competitive active site inhibitors but can still process the natural substrates with enough efficiency for viral survival. In previous works we have developed the "substrate envelope" hypothesis, which posits that inhibitors should be less susceptible to drug resistance if they better mimic the natural substrate molecular recognition features. In this work, we perform molecular dynamics simulations on four native substrates bound to NS3/4A and discover a clearly conserved dynamic substrate envelope. We show that the most severe drug resistance mutations in NS3/4A occur at residues that are outside the substrate envelope. Comparative analysis of three NS3/4A inhibitors reveals structural and dynamic characteristics of inhibitors that could lead to resistance. We also suggest inhibitor modifications to improve resistance profiles based on the dynamic substrate envelope. This study provides a general framework for guiding the development of novel inhibitors that will be more robust against resistance by mimicking the static and dynamic binding characteristics of natural substrates.
Collapse
Affiliation(s)
- Ayşegül Ozen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Woody Sherman
- Schrödinger, Inc., 120 West 45th Street, New York, NY 10036, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| |
Collapse
|
38
|
Hepatitis C virus RNA replication and virus particle assembly require specific dimerization of the NS4A protein transmembrane domain. J Virol 2013; 88:628-42. [PMID: 24173222 DOI: 10.1128/jvi.02052-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) NS4A is a single-pass transmembrane (TM) protein essential for viral replication and particle assembly. The sequence of the NS4A TM domain is highly conserved, suggesting that it may be important for protein-protein interactions. To test this hypothesis, we measured the potential dimerization of the NS4A TM domain in a well-characterized two-hybrid TM protein interaction system. The NS4A TM domain exhibited a strong homotypic interaction that was comparable in affinity to glycophorin A, a well-studied human blood group antigen that forms TM homodimers. Several mutations predicted to cluster on a common surface of the NS4A TM helix caused significant reductions in dimerization, suggesting that these residues form an interface for NS4A dimerization. Mutations in the NS4A TM domain were further examined in the JFH-1 genotype 2a replicon system; importantly, all mutations that destabilized NS4A dimers also caused defects in RNA replication and/or virus assembly. Computational modeling of NS4A TM interactions suggests a right-handed dimeric interaction of helices with an interface that is consistent with the mutational effects. Furthermore, defects in NS4A oligomerization and virus particle assembly of two mutants were rescued by NS4A A15S, a TM mutation recently identified through forward genetics as a cell culture-adaptive mutation. Together, these data provide the first example of a functionally important TM dimer interface within an HCV nonstructural protein and reveal a fundamental role of the NS4A TM domain in coordinating HCV RNA replication and virus particle assembly.
Collapse
|
39
|
Hartjen P, Höchst B, Heim D, von der Kammer H, Lucke J, Reinholz M, Baier A, Smeets R, Wege H, Borowski P, Schulze Zur Wiesch J. The NTPase/helicase domain of hepatitis C virus nonstructural protein 3 inhibits protein kinase C independently of its NTPase activity. Cell Mol Biol Lett 2013; 18:447-58. [PMID: 23893289 PMCID: PMC6275940 DOI: 10.2478/s11658-013-0099-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 07/17/2013] [Indexed: 11/20/2022] Open
Abstract
Helicase motif VI is a short arginine-rich motif within the NTPase/helicase domain of the non-structural protein 3 (NS3) of the hepatitis C virus (HCV). We previously demonstrated that it reduces the catalytic activity and intracellular shuttling of protein kinase C (PKC). Thus, NS3-mediated PKC inhibition may be involved in HCV-associated hepatocellular carcinoma (HCC). In this study, we expand on our earlier results, which were obtained in experiments with short fragments of NS3, to show for the first time that the catalytically active, longer C-terminal NTPase/helicase of NS3 acts as a potent PKC inhibitor in vitro. PKC inhibition assays with the NTPase-inactive mutant NS3h-D1316A revealed a mixed type kinetic inhibition pattern. A broad range of 11 PKC isotypes was tested and all of the PKC isotypes were inhibited with IC₅₀-values in the low micromolar range. These findings were confirmed for the wild-type NTPase/helicase domain in a non-radiometric PKC inhibition assay with ATP regeneration to rule out any effect of ATP hydrolysis caused by its NTPase activity. PKCα was inhibited with a micromolar IC₅₀ in this assay, which compares well with our result for NS3h-D1316A (IC₅₀ = 0.7 μM). In summary, these results confirm that catalytically active NS3 NTPase/helicase can act in an analogous manner to shorter NS3 fragments as a pseudosubstrate inhibitor of PKC.
Collapse
Affiliation(s)
- Philip Hartjen
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Shadrick WR, Mukherjee S, Hanson AM, Sweeney NL, Frick DN. Aurintricarboxylic acid modulates the affinity of hepatitis C virus NS3 helicase for both nucleic acid and ATP. Biochemistry 2013; 52:6151-9. [PMID: 23947785 DOI: 10.1021/bi4006495] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aurintricarboxylic acid (ATA) is a potent inhibitor of many enzymes needed for cell and virus replication, such as polymerases, helicases, nucleases, and topoisomerases. This study examines how ATA interacts with the helicase encoded by the hepatitis C virus (HCV) and reveals that ATA interferes with both nucleic acid and ATP binding to the enzyme. We show that ATA directly binds HCV helicase to prevent the enzyme from interacting with nucleic acids and to modulate the affinity of HCV helicase for ATP, the fuel for helicase action. Amino acid substitutions in the helicase DNA binding cleft or its ATP binding site alter the ability of ATA to disrupt helicase-DNA interactions. These data, along with molecular modeling results, support the notion that an ATA polymer binds between Arg467 and Glu493 to prevent the helicase from binding either ATP or nucleic acids. We also characterize how ATA affects the kinetics of helicase-catalyzed ATP hydrolysis, and thermodynamic parameters describing the direct interaction between HCV helicase and ATA using microcalorimetry. The thermodynamics of ATA binding to HCV helicase reveal that ATA binding does not mimic nucleic acid binding in that ATA binding is driven by a smaller enthalpy change and an increase in entropy.
Collapse
Affiliation(s)
- William R Shadrick
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | | | | | | | | |
Collapse
|
41
|
Linder P, Fuller-Pace FV. Looking back on the birth of DEAD-box RNA helicases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:750-5. [PMID: 23542735 DOI: 10.1016/j.bbagrm.2013.03.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 12/20/2022]
Abstract
DEAD-box proteins represent the largest family of RNA helicases, present in all three kingdoms of life. They are involved in a variety of processes involving RNA metabolism and in some instances also in processes that use guide RNAs. Since their first descriptions in the late 1980s, the perception of their molecular activities has dramatically changed. At the time when only eight proteins with 9 conserved motifs constituted the DEAD-box protein family, it was the biochemical characterization of mammalian eIF4A that first suggested a local unwinding activity. This was confirmed in vitro using partially double stranded RNA substrates with the unexpected result of a bidirectional unwinding activity. A real change of paradigm from the classical helicase activity to localized RNA unwinding occurred with the publication of the vasa•RNA structure with a bend in the RNA substrate and the insightful work from several laboratories demonstrating local unwinding without translocation. Finally, elegant work on the exon-junction complex revealed how DEAD-box proteins can bind to RNA to serve as clamps to function as nucleation centers to form RNP complexes. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.
Collapse
Affiliation(s)
- Patrick Linder
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.
| | | |
Collapse
|
42
|
Shadrick WR, Ndjomou J, Kolli R, Mukherjee S, Hanson AM, Frick DN. Discovering new medicines targeting helicases: challenges and recent progress. ACTA ACUST UNITED AC 2013; 18:761-81. [PMID: 23536547 PMCID: PMC4427233 DOI: 10.1177/1087057113482586] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Helicases are ubiquitous motor proteins that separate and/or rearrange nucleic acid duplexes in reactions fueled by adenosine triphosphate (ATP) hydrolysis. Helicases encoded by bacteria, viruses, and human cells are widely studied targets for new antiviral, antibiotic, and anticancer drugs. This review summarizes the biochemistry of frequently targeted helicases. These proteins include viral enzymes from herpes simplex virus, papillomaviruses, polyomaviruses, coronaviruses, the hepatitis C virus, and various flaviviruses. Bacterial targets examined include DnaB-like and RecBCD-like helicases. The human DEAD-box protein DDX3 is the cellular antiviral target discussed, and cellular anticancer drug targets discussed are the human RecQ-like helicases and eIF4A. We also review assays used for helicase inhibitor discovery and the most promising and common helicase inhibitor chemotypes, such as nucleotide analogues, polyphenyls, metal ion chelators, flavones, polycyclic aromatic polymers, coumarins, and various DNA binding pharmacophores. Also discussed are common complications encountered while searching for potent helicase inhibitors and possible solutions for these problems.
Collapse
Affiliation(s)
- William R Shadrick
- Department of Chemistry & Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | | | | | | | | | | |
Collapse
|
43
|
Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid. Biophys J 2013; 103:1343-53. [PMID: 22995507 DOI: 10.1016/j.bpj.2012.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/01/2012] [Accepted: 08/06/2012] [Indexed: 01/14/2023] Open
Abstract
The NS3 helicase of Hepatitis C virus is an ATP-fueled molecular motor that can translocate along single-stranded (ss) nucleic acid, and unwind double-stranded nucleic acids. It makes a promising antiviral target and an important prototype system for helicase research. Despite recent progress, the detailed mechanism of NS3 helicase remains unknown. In this study, we have combined coarse-grained (CG) and atomistic simulations to probe the translocation mechanism of NS3 helicase along ssDNA. At the residue level of detail, our CG simulations have captured functionally important interdomain motions of NS3 helicase and reproduced single-base translocation of NS3 helicase along ssDNA in the 3'-5' direction, which is in good agreement with experimental data and the inchworm model. By combining the CG simulations with residue-specific perturbations to protein-DNA interactions, we have identified a number of key residues important to the translocation machinery that agree with previous structural and mutational studies. Additionally, our atomistic simulations with targeted molecular dynamics have corroborated the findings of CG simulations and further revealed key protein-DNA hydrogen bonds that break/form during the transitions. This study offers, to our knowledge, the most detailed and realistic simulations of translocation mechanism of NS3 helicase. The simulation protocol established in this study will be useful for designing inhibitors that target the translocation machinery of NS3 helicase, and for simulations of a variety of nucleic-acid-based molecular motors.
Collapse
|
44
|
Abstract
The current treatment for hepatitis C virus (HCV) genotype 1 chronic infection is the addition of direct-acting antivirals (DAA) with a protease inhibitor (telaprevir or boceprevir) to the pegylated interferon (PEG-IFN) plus ribavirin (RBV) regimen. Major progress has been made in the past few years: numerous ongoing trials with different compounds, increasing sustained virological response (SVR) rates with oral regimens and shortened treatment duration. Combinations of antivirals with additive potency that lack cross-resistance and with a good safety profile may provide new regimens in the future to make HCV the first chronic viral infection to be eradicated worldwide with a finite duration of combination DAA therapy without IFN.
Collapse
Affiliation(s)
- Tarik Asselah
- Hepatology Department, AP-HP, University Paris Diderot 7 and INSERM U773, CRB3, Beaujon Hospital, Clichy, France.
| | | |
Collapse
|
45
|
Structure and Mechanisms of SF1 DNA Helicases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 767:17-46. [PMID: 23161005 DOI: 10.1007/978-1-4614-5037-5_2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Superfamily I is a large and diverse group of monomeric and dimeric helicases defined by a set of conserved sequence motifs. Members of this class are involved in essential processes in both DNA and RNA metabolism in all organisms. In addition to conserved amino acid sequences, they also share a common structure containing two RecA-like motifs involved in ATP binding and hydrolysis and nucleic acid binding and unwinding. Unwinding is facilitated by a "pin" structure which serves to split the incoming duplex. This activity has been measured using both ensemble and single-molecule conditions. SF1 helicase activity is modulated through interactions with other proteins.
Collapse
|
46
|
Suhasini AN, Brosh RM. Disease-causing missense mutations in human DNA helicase disorders. Mutat Res 2012; 752:138-152. [PMID: 23276657 DOI: 10.1016/j.mrrev.2012.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/18/2012] [Accepted: 12/19/2012] [Indexed: 01/22/2023]
Abstract
Helicases have important roles in nucleic acid metabolism, and their prominence is marked by the discovery of genetic disorders arising from disease-causing mutations. Missense mutations can yield unique insight to molecular functions and basis for disease pathology. XPB or XPD missense mutations lead to Xeroderma pigmentosum, Cockayne's syndrome, Trichothiodystrophy, or COFS syndrome, suggesting that DNA repair and transcription defects are responsible for clinical heterogeneity. Complex phenotypes are also observed for RECQL4 helicase mutations responsible for Rothmund-Thomson syndrome, Baller-Gerold syndrome, or RAPADILINO. Bloom's syndrome causing missense mutations are found in the conserved helicase and RecQ C-terminal domain of BLM that interfere with helicase function. Although rare, patient-derived missense mutations in the exonuclease or helicase domain of Werner syndrome protein exist. Characterization of WRN separation-of-function mutants may provide insight to catalytic requirements for suppression of phenotypes associated with the premature aging disorder. Characterized FANCJ missense mutations associated with breast cancer or Fanconi anemia interfere with FANCJ helicase activity required for DNA repair and the replication stress response. For example, a FA patient-derived mutation in the FANCJ Iron-Sulfur domain was shown to uncouple its ATPase and translocase activity from DNA unwinding. Mutations in DDX11 (ChlR1) are responsible for Warsaw Breakage syndrome, a recently discovered autosomal recessive cohesinopathy. Ongoing and future studies will address clinically relevant helicase mutations and polymorphisms, including those that interfere with key protein interactions or exert dominant negative phenotypes (e.g., certain mutant alleles of Twinkle mitochondrial DNA helicase). Chemical rescue may be an approach to restore helicase activity in loss-of-function helicase disorders. Genetic and biochemical analyses of disease-causing missense mutations in human helicase disorders have led to new insights to the molecular defects underlying aberrant cellular and clinical phenotypes.
Collapse
Affiliation(s)
- Avvaru N Suhasini
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Drive, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, 251 Bayview Drive, Baltimore, MD 21224, USA.
| |
Collapse
|
47
|
Mukherjee S, Hanson AM, Shadrick WR, Ndjomou J, Sweeney NL, Hernandez JJ, Bartczak D, Li K, Frankowski KJ, Heck JA, Arnold LA, Schoenen FJ, Frick DN. Identification and analysis of hepatitis C virus NS3 helicase inhibitors using nucleic acid binding assays. Nucleic Acids Res 2012; 40:8607-21. [PMID: 22740655 PMCID: PMC3458564 DOI: 10.1093/nar/gks623] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Typical assays used to discover and analyze small molecules that inhibit the hepatitis C virus (HCV) NS3 helicase yield few hits and are often confounded by compound interference. Oligonucleotide binding assays are examined here as an alternative. After comparing fluorescence polarization (FP), homogeneous time-resolved fluorescence (HTRF®; Cisbio) and AlphaScreen® (Perkin Elmer) assays, an FP-based assay was chosen to screen Sigma’s Library of Pharmacologically Active Compounds (LOPAC) for compounds that inhibit NS3-DNA complex formation. Four LOPAC compounds inhibited the FP-based assay: aurintricarboxylic acid (ATA) (IC50 = 1.4 μM), suramin sodium salt (IC50 = 3.6 μM), NF 023 hydrate (IC50 = 6.2 μM) and tyrphostin AG 538 (IC50 = 3.6 μM). All but AG 538 inhibited helicase-catalyzed strand separation, and all but NF 023 inhibited replication of subgenomic HCV replicons. A counterscreen using Escherichia coli single-stranded DNA binding protein (SSB) revealed that none of the new HCV helicase inhibitors were specific for NS3h. However, when the SSB-based assay was used to analyze derivatives of another non-specific helicase inhibitor, the main component of the dye primuline, it revealed that some primuline derivatives (e.g. PubChem CID50930730) are up to 30-fold more specific for HCV NS3h than similarly potent HCV helicase inhibitors.
Collapse
Affiliation(s)
- Sourav Mukherjee
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
RNA helicases unwind their RNA substrates in an ATP-dependent reaction, and are central to all cellular processes involving RNA. They have important roles in viral life cycles, where RNA helicases are either virus-encoded or recruited from the host. Vertebrate RNA helicases sense viral infections, and trigger the innate antiviral immune response. RNA helicases have been implicated in protozoic, bacterial and fungal infections. They are also linked to neurological disorders, cancer, and aging processes. Genome-wide studies continue to identify helicase genes that change their expression patterns after infection or disease outbreak, but the mechanism of RNA helicase action has been defined for only a few diseases. RNA helicases are prognostic and diagnostic markers and suitable drug targets, predominantly for antiviral and anti-cancer therapies. This review summarizes the current knowledge on RNA helicases in infection and disease, and their growing potential as drug targets.
Collapse
Affiliation(s)
- Lenz Steimer
- University of Muenster, Institute for Physical Chemistry, Muenster, Germany
| | | |
Collapse
|
49
|
Asselah T, Marcellin P. Direct acting antivirals for the treatment of chronic hepatitis C: one pill a day for tomorrow. Liver Int 2012; 32 Suppl 1:88-102. [PMID: 22212578 DOI: 10.1111/j.1478-3231.2011.02699.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chronic hepatitis C is one of the leading causes of chronic liver disease with approximately 170 million people infected worldwide. Sustained virological response (SVR) is equivalent to viral eradication and associated with a reduction in the risk of cirrhosis. Nowadays the treatment for hepatitis C virus (HCV) genotype 1 chronic infection is the addition of direct acting antivirals (DAA) with a protease inhibitor (telaprevir or boceprevir) to the pegylated interferon (PEG-IFN) plus ribavirin (RBV) regimen. The future management of patients with these new molecules will require good clinical practice, knowledge of indications, management of side effects and monitoring for antiviral resistance. Certain major medical needs are still unmet and require studies in special populations (HIV-HCV coinfected patients, transplanted patients, etc.…) and also in HCV non-1 genotype patients and in non-responders. Second generation DAA are in development. Combinations of antivirals with additive potency that lack cross resistance and with a good safety profile may provide new regimens in the future to make HCV the first chronic viral infection eradicated worldwide with a finite duration of combination DAA therapy without IFN. The aim of this review is to summarize mechanisms of action and results obtained with DAAs.
Collapse
Affiliation(s)
- Tarik Asselah
- Service d'hépatologie, Hôpital Beaujon, APHP, University Paris-Diderot and INSERM CRB3, Clichy, France.
| | | |
Collapse
|
50
|
Wu Y, Brosh RM. DNA helicase and helicase-nuclease enzymes with a conserved iron-sulfur cluster. Nucleic Acids Res 2012; 40:4247-60. [PMID: 22287629 PMCID: PMC3378879 DOI: 10.1093/nar/gks039] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Conserved Iron-Sulfur (Fe-S) clusters are found in a growing family of metalloproteins that are implicated in prokaryotic and eukaryotic DNA replication and repair. Among these are DNA helicase and helicase-nuclease enzymes that preserve chromosomal stability and are genetically linked to diseases characterized by DNA repair defects and/or a poor response to replication stress. Insight to the structural and functional importance of the conserved Fe-S domain in DNA helicases has been gleaned from structural studies of the purified proteins and characterization of Fe-S cluster site-directed mutants. In this review, we will provide a current perspective of what is known about the Fe-S cluster helicases, with an emphasis on how the conserved redox active domain may facilitate mechanistic aspects of helicase function. We will discuss testable models for how the conserved Fe-S cluster might operate in helicase and helicase-nuclease enzymes to conduct their specialized functions that help to preserve the integrity of the genome.
Collapse
Affiliation(s)
- Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, Saskatoon, Saskatchewan, S7N 5E5, Canada.
| | | |
Collapse
|