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Nikolaeva LI, Belyavtsev AN, Shevchenko NG, Stuchinskaya MD, Samokhvalov EI, Dedova AV, Sapronov GV, Shastina NS, Kuprianov VV. [The analysis of immunoreactivity of individual B-cell epitopes of hepatitis C virus (Flaviviridae: Hepacivirus: Hepatitis С virus) NS4a antigen]. Vopr Virusol 2022; 67:237-245. [PMID: 35831966 DOI: 10.36233/0507-4088-115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Chronic viral hepatitis C (CHC) is a ubiquitous infectious disease, a significant limitation of which WHO attributes to the use of a new highly effective antiviral therapy. Previously, two B-cell epitopes were identified in NS4a antigen of the hepatitis C virus (HCV). It was shown that certain titers of antibodies (ABs) to the extended C-terminal epitope (1687-1718 a.a.) can predict a high probability of achieving a sustained virological response (SVR) to standard therapy with pegylated interferon-α and ribavirin.The aim of the work was to determine immunoreactivity of two B-cell epitopes (middle and C-terminal) of NS4a antigen, and to estimate a possible association of ABs to them with the achievement of SVR after standard interferon therapy and treatment with direct antiviral drugs (DAAs) daclatasvir and sofosbuvir (velpanat). MATERIALS AND METHODS Blood serum samples of patients with CHC (n = 113), of which 55 participants received standard interferon therapy, 50 received velpanate treatment, the remaining 8 received no therapy were examined. The middle B-cell epitope (positions 24-34 a.a.) of NS4a was synthesized by the solid-phase method, while the C-terminal epitope (34-54 a.a.) was obtained using genetically engineered techniques. Enzyme immunoassay (ELISA) testing of the sera collected before treatment was performed for the two selected epitopes according to the conventional methods. RESULTS The antibodies to the C-terminal epitope were detected significantly more frequently than those to the middle one (p = 0.01) when analyzing the blood sera of patients (n = 113). The presence of ABs to the C-terminal epitope in the serum samples of participants who completed standard interferon therapy was associated with the achievement of SVR (p = 0.0245). In the blood sera of participants who completed therapy with velpanate, an association of the presence of ABs to the C-terminal epitope with the achievement of SVR was also established (p < 0.0001). The presence of ABs to the middle B epitope was not associated with the achievement of SVR, regardless of the therapy used. DISCUSSION The observed difference in the immunoreactivity of the two B-cell determinants may be associated with the localization of the nearest Th-epitopes, the sensitivity of NS4a antigen to proteolytic enzymes, and the peculiarities of epitope presentation by antigen-presenting cells. However, it should be noted that the immunoreactivity of the middle B-epitope is poorly studied. Although the association of ABs to the C-terminal epitope with the achievement of SVR has been shown by several scientific teams, the detailed molecular mechanism of their influence on the effectiveness of therapy is unclear. CONCLUSION In CHC, ABs to the C-terminal epitope of NS4a are produced more frequently than those to the median epitope. The presence of ABs to the C-terminal epitope is a predictive marker of a high probability of achieving SVR, regardless of the type of therapy and antibody titer.
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Affiliation(s)
- L I Nikolaeva
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - A N Belyavtsev
- «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia; FSBEI HE «MIREA - Russian Technology University»
| | - N G Shevchenko
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - M D Stuchinskaya
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - E I Samokhvalov
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - A V Dedova
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - G V Sapronov
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia; FSBEI FPE «Russian Medical Academy of Continuous Professional Education» of the Ministry of Health of Russia
| | - N S Shastina
- FSBEI HE «MIREA - Russian Technology University»
| | - V V Kuprianov
- FSBI «National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya» of the Ministry of Health of Russia; Federal Research Center «Fundamentals of Biotechnology» of the Russian Academy of Sciences
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Belyavtsev AN, Shastina NS, Kupriyanov VV, Nikolaeva LI, Melnikova MV, Kolesanova EF, Shimchishina MY, Kapustin IV. Effect of Lipid Components on Immunogenicity of Synthetic Fragment of Hepatitis C Virus NS4A Antigen. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Belyavtsev AN, Melnikova MV, Shevchenko NG, Sapronov GV, Vahrenev RG, Shastina NS, Kolesanova EF, Nikolaeva LI. Synthesis and Analysis of Properties of an Immunogenic Fragment from NS4A Polypeptide of Hepatitis C Virus. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract—
The work is aimed at the synthesis and analysis from NS4A of hepatitis C virus (HCV) antigen peptide fragment that contains a conserved B-cell and T-helper epitopes. The 24-mer peptide VIVGRIILSGRPAVIPDREVLYRK-NH2, which contains the main immunogenic site 24–46 of HCV NS4A antigen (corresponding to the 1681–1703 amino acid residues of the HCV polypeptide), subtype 1b, has been prepared via solid-phase synthesis according to the Fmoc-protocol. Particles with diameters of 73 ± 10 nm (30%) and 236 ± 5 nm (70%) have been detected in the water solution of the highly purified peptide (0.5 mg/mL) by dynamic light scattering. The polydispersity index of 0.377 ± 0.012 implies the existence of heterogeneity because of the aggregation of the peptide molecules. The ζ-potential of the peptide aggregates has been determined as 7.0 ± 0.5 mV by means of electrophoretic light scattering. These data confirm the possibility for the development of a nanoscale liposome form of the peptide preparation. Immunoreactivity of the synthesized highly purified peptide has been studied with the use of blood sera of patients with chronic hepatitis C. Antipeptide immunoglobulins G have been detected in 41.7% of serum samples. Thus, this peptide has been shown to reproduce at least one B-epitope, to which antibodies are raised during natural HCV infection. The synthesized 24-mer peptide is a promising candidate for further research and for use as a potential immunogen for the design of a nanoscale therapeutic immunogenic liposomal peptide composition with synthetic lipids as an adjuvant.
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Shahid I, Almalki WH, Ibrahim MM, Alghamdi SA, Mukhtar MH, Almalki SSR, Alkahtani SA, Alhaidari MS. Characterization of In vitro inhibitory effects of consensus short interference RNAs against non-structural 5B gene of hepatitis C virus 1a genotype. Indian J Med Microbiol 2019; 36:494-503. [PMID: 30880695 DOI: 10.4103/ijmm.ijmm_17_146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Purpose Chronic hepatitis C has infected approximately 170 million people worldwide. The novel direct-acting antivirals have proven their clinical efficacy to treat hepatitis C infection but still very expensive and beyond the financial range of most infected patients in low income and even resource replete nations. This study was conducted to establish an in vitro stable human hepatoma 7 (Huh-7) cell culture system with consistent expression of the non-structural 5B (NS5B) protein of hepatitis C virus (HCV) 1a genotype and to explore inhibitory effects of sequence-specific short interference RNA (siRNA) targeting NS5B in stable cell clones, and against viral replication in serum-inoculated Huh-7 cells. Materials and Methods In vitro stable Huh-7 cells with persistent expression of NS5B protein was produced under gentamycin (G418) selection. siRNAs inhibitory effects were determined by analysing NS5B expression at mRNA and protein level through reverse transcription-polymerase chain reaction (PCR), quantitative real-time PCR, and Western blot, respectively. Statistical significance of data (NS5B gene suppression) was performed using SPSS software (version 16.0, SPSS Inc.). Results siRNAs directed against NS5B gene significantly decreased NS5B expression at mRNA and protein levels in stable Huh-7 cells, and a vivid decrease in viral replication was also exhibited in serum-infected Huh-7 cells. Conclusions Stable Huh-7 cells persistently expressing NS5B protein should be helpful for molecular pathogenesis of HCV infection and development of anti-HCV drug screening assays. The siRNA was effective against NS5B and could be considered as an adjuvant therapy along with other promising anti-HCV regimens.
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Affiliation(s)
- Imran Shahid
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al Qura University, Makkah, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al Qura University, Makkah, Saudi Arabia
| | - Munjed M Ibrahim
- Department of Pharmaceutical Chemistry, College of Pharmacy, Umm Al Qura University, Makkah, Saudi Arabia
| | - Sultan Ahmad Alghamdi
- Infection Control Department, King Fahd Hospital, Ministry of Health, Jeddah, Saudi Arabia
| | - Mohammed H Mukhtar
- Department of Biochemistry, College of Medicine, Umm Al-Qura Univeristy, Makkah, Saudi Arabia
| | - Shaia Saleh R Almalki
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al Baha University, Al Baha, Saudi Arabia
| | - Saad Ahmed Alkahtani
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Mohammad S Alhaidari
- Pharmaceutical Care Department, King Fahad Hospital, Ministry of Health, Madinah, Saudi Arabia
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Hussain A, Idrees M, Asif M, Ali L, Rasool M. Phylogenetic and 2D/3D Analysis of HCV 1a NS4A Gene/Protein in Pakistani Isolates. HEPATITIS MONTHLY 2015; 15:e19936. [PMID: 26288631 PMCID: PMC4532788 DOI: 10.5812/hepatmon.15(6)2015.19936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 07/19/2014] [Accepted: 09/11/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND The nonstructural protein NS4A of hepatitis C virus is composed of 54 amino acids. This small size protein has vital role in many cellular functions. The most important reported function is being a cofactor of viral enzymes serine protease and helicase. OBJECTIVES The objective of this study was to analyze the phylogenetic variation, its impact in terms of translation and any functional change in protein structure at primary 2D/3D structure using computational tools from Pakistani patients isolates. MATERIALS AND METHODS Patient sera infected with Hepatitis C virus, genotype 1A, were obtained from Molecular Diagnostics lab, CEMB, University of the Punjab Lahore by using BD Vacutainer collection tubes (Becton Dickenson). RESULTS Phylogenetic analysis of the gene revealed that Pakistani 1a HCV strains are in the start of third cluster and there is a difference between inter Pakistani isolates at primary, secondary and tertiary levels. CONCLUSIONS Mutations were present in the central domain of NS4A (amino acids 21 - 34).
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Affiliation(s)
- Abrar Hussain
- Department of Biotechnology and Informtics, BUITEMS, Quetta, Pakistan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Corresponding Author: Muhammad Idrees, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan. Tel: +92-3214769212, E-mail:
| | - Muhammad Asif
- Department of Biotechnology and Informtics, BUITEMS, Quetta, Pakistan
| | - Liaqat Ali
- Division of Infectious Diseases, Department of Internal Medicine II, University Hospital Freiburg, Freiburg, Germany
- Faculty of Biology, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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Shahid I, AlMalki WH, R. Almalki SS, AlTurkestany IM, AlGhamdi HA, AlMenshawi SA. Inhibition of Hepatitis C Virus Genotype 1a Non-Structural Proteins by Small Interference RNA in Human Hepatoma Cell Lines. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/pp.2015.611053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Aziz H, Raza A, Murtaza S, Waheed Y, Khalid A, Irfan J, Samra Z, Athar MA. Molecular epidemiology of hepatitis C virus genotypes in different geographical regions of Punjab Province in Pakistan and a phylogenetic analysis. Int J Infect Dis 2013. [PMID: 23183233 DOI: 10.1016/j.ijid.2012.09.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) is a causative agent of chronic liver disease, cirrhosis, and hepatocellular carcinoma. In Pakistan, more than 10 million people are living with HCV. Very little is known about the genotype distribution in Punjab Province, the largest province of Pakistan. Pretreatment genotype identification is very important, as different HCV genotypes respond differently to interferon therapy. METHODS In this study we performed HCV genotyping for 1537 HCV-infected patients from different districts of Punjab Province, Pakistan. Sequencing of partial HCV NS5B sequences from 14 samples belonging to genotypes 3 and 1 was also done. A sequence comparison was made of our reported sequences with those reported in the National Center for Biotechnology Information (NCBI), and a phylogenetic tree was constructed. RESULTS Our study showed that the most frequent HCV genotype was 3a (in 88.1% of infected individuals), followed by 1a (3.5%), 3b (3.0%), 1b (0.8%), and 2a (1.0%). A mixed genotype infection was found in 3.6% of infected individuals, with 0.3% living with 1a + 1b co-infection, 3.1% with 3a+3b, and 0.2% suffering from 3a+1b co-infection. The sequence comparison showed that HCV NS5B motif B residues G283, T287, and N291 were highly conserved in both genotype 1 and genotype 3 sequences, while the motif B residue T286 was mutated to proline in all the genotype 3 sequences. The GDD motif, which forms the catalytic pocket and binding site for the divalent cations, was highly conserved in all the reported sequences. The phylogenetic tree suggests clustering of genotype 1 sequences with sequences from the USA, UK, Germany, and France, while genotype 3 sequences are clustered with sequences from Japan and the UK. CONCLUSIONS The major prevalent genotype in Punjab Province of Pakistan was genotype 3a, followed by genotype 1a, and only 3.6% of infected individuals had a mixed genotype infection. Sequencing of the HCV NS5B gene suggested that the active site residues were highly conserved in all the reported sequences. Our sequences, which are clustered with sequences from the USA, UK, France, and Japan, show the diversity in origin of the different genotypes prevalent in Pakistan.
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Affiliation(s)
- Hafsa Aziz
- Diagnostic Laboratories, Nuclear Medicine Oncology and Radiotherapy Institute, Hanna Road, G-8/3, Islamabad, Pakistan.
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Waheed Y, Saeed U, Anjum S, Afzal MS, Ashraf M. Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Prote in. HEPATITIS MONTHLY 2012; 12:e6142. [PMID: 23087757 PMCID: PMC3475062 DOI: 10.5812/hepatmon.6142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 07/31/2012] [Accepted: 08/14/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) is a plus stranded RNA virus which encodes 10 different genes. The HCV NS5B gene encodes a polymerase, which is responsible for the replication of the virus and is a potential target for the development of antiviral agents. HCV has a high mutation rate and is classified into six major genotypes. OBJECTIVES The aim of this study was to draw a representing consensus sequence of each HCV genotype, align all six consensus sequences to draw a global consensus sequence and also study the highly conserved residues. MATERIALS AND METHODS 236 HCV NS5B sequences, belonging to all six genotypes, reported from all over the world were aligned then a representing phylogenetic tree wasdrawn. RESULTS The active site residues D220, D225, D318 and D319, which bind the divalent cations, are highly conserved among all the HCV genotypes. The other catalytic pocket residues, R158, S367, R386, and T390 and R394, which interact with the triphosphate of NTPs, are also highly conserved while T390 is mutated to valine in the genotype 5. The motif B residues G283, T286, T287 and N291, which take part in sugar selection by RdRp, are also highly conserved except for T286 which is mutated to proline in the genotypes 3 and 6. The residues E18, Y191, C274, Y276 and H502, which take part in primer/template interaction, are also high conserved except for H502 which is mutated to serine in genotype 2. High variation in all the six consensus sequences was observed in a 12 amino acid beta hairpin loop, which interacts with the double stranded RNA. Nine different peptides from the highly conserved regions of HCV NS5B protein were drawn which can be used as a peptide vaccine. The HCV NS5B phylogenetic tree shows the clusters of different genotypes and their evolutionary association. CONCLUSIONS In spite of a high mutation rate in HCV, the residues which are present in the catalytic pocket, sugar selection and template/primer interaction are highly conserved. These are target sites for the development of antiviral agents or peptide vaccines. The phylogenetic analysis suggests that different HCV genotypes have been evolved from the genotype 1a.
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Affiliation(s)
- Yasir Waheed
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Corresponding author: Yasir Waheed, Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, (44000), Pakistan. Tel.: +92-3005338171, Fax: +92-5190856102, E-mail:
| | - Umar Saeed
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Sadia Anjum
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Mohammad Sohail Afzal
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Ashraf
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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