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Ghasemlou A, Uskoković V, Sefidbakht Y. Exploration of potential inhibitors for SARS-CoV-2 Mpro considering its mutants via structure-based drug design, molecular docking, MD simulations, MM/PBSA, and DFT calculations. Biotechnol Appl Biochem 2023; 70:439-457. [PMID: 35642754 DOI: 10.1002/bab.2369] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/21/2022] [Indexed: 11/08/2022]
Abstract
The main protease (Mpro) of SARS-COV-2 plays a vital role in the viral life cycle and pathogenicity. Due to its specific attributes, this 3-chymotrypsin like protease can be a reliable target for the drug design to combat COVID-19. Since the advent of COVID-19, Mpro has undergone many mutations. Here, the impact of 10 mutations based on their frequency and five more based on their proximity to the active site was investigated. For comparison purposes, the docking process was also performed against the Mpros of SARS-COV and MERS-COV. Four inhibitors with the highest docking score (11b, α-ketoamide 13b, Nelfinavir, and PF-07321332) were selected for the structure-based ligand design via fragment replacement, and around 2000 new compounds were thus obtained. After the screening of these new compounds, the pharmacokinetic properties of the best ones were predicted. In the last step, comparative molecular dynamics (MD) simulations, molecular mechanics Poisson-Boltzmann surface area calculations (MM/PBSA), and density functional theory calculations were performed. Among the 2000 newly designed compounds, three of them (NE1, NE2, and NE3), which were obtained by modifications of Nelfinavir, showed the highest affinity against all the Mpro targets. Together, NE1 compound is the best candidate for follow-up Mpro inhibition and drug development studies.
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Affiliation(s)
| | - Vuk Uskoković
- TardigradeNano, LLC, Irvine, California, USA.,Department of Mechanical Engineering, San Diego State University, San Diego, California, USA
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
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2
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Zheng C, Schneider M, Marion A, Antes I. The Q41R mutation in the HCV-protease enhances the reactivity towards MAVS by suppressing non-reactive pathways. Phys Chem Chem Phys 2022; 24:2126-2138. [PMID: 35029245 DOI: 10.1039/d1cp05002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental findings pointed out a new mutation in the HCV protease, Q41R, responsible for a significant enhancement of the enzyme's reactivity towards the mitochondrial antiviral-signaling protein (MAVS). The Q41R mutation is located rather far from the active site, and its involvement in the overall reaction mechanism is thus unclear. We used classical molecular dynamics and QM/MM to study the acylation reaction of HCV NS3/4A protease variants bound to MAVS and the NS4A/4B substrate and uncovered the indirect mechanism by which the Q41R mutation plays a critical role in the efficient cleavage of the substrate. Our simulations reveal that there are two major conformations of the MAVS H1'(p) residue for the wild type protease and only one conformation for the Q41R mutant. The conformational space of H1'(p) is restricted by the Q41R mutation due to a π-π stacking between H1'(p) and R41 as well as a strong hydrogen bond between the backbone of H57 and the side chain of R41. Further QM/MM calculations indicate that the complex with the conformation ruled out by the Q41R substitution is a non-reactive species due to its higher free energy barrier for the acylation reaction. Based on our calculations, we propose a kinetic mechanism that explains experimental data showing an increase of apparent rate constants for MAVS cleavage in Q41R mutants. Our model predicts that the non-reactive conformation of the enzyme-substrate complex modulates reaction kinetics like an uncompetitive inhibitor.
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Affiliation(s)
- Chen Zheng
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Markus Schneider
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Antoine Marion
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Middle East Technical University, Department of Chemistry, Ankara 06800, Turkey.
| | - Iris Antes
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
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3
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Citarella A, Scala A, Piperno A, Micale N. SARS-CoV-2 M pro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors. Biomolecules 2021; 11:607. [PMID: 33921886 PMCID: PMC8073203 DOI: 10.3390/biom11040607] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
The uncontrolled spread of the COVID-19 pandemic caused by the new coronavirus SARS-CoV-2 during 2020-2021 is one of the most devastating events in the history, with remarkable impacts on the health, economic systems, and habits of the entire world population. While some effective vaccines are nowadays approved and extensively administered, the long-term efficacy and safety of this line of intervention is constantly under debate as coronaviruses rapidly mutate and several SARS-CoV-2 variants have been already identified worldwide. Then, the WHO's main recommendations to prevent severe clinical complications by COVID-19 are still essentially based on social distancing and limitation of human interactions, therefore the identification of new target-based drugs became a priority. Several strategies have been proposed to counteract such viral infection, including the repurposing of FDA already approved for the treatment of HIV, HCV, and EBOLA, inter alia. Among the evaluated compounds, inhibitors of the main protease of the coronavirus (Mpro) are becoming more and more promising candidates. Mpro holds a pivotal role during the onset of the infection and its function is intimately related with the beginning of viral replication. The interruption of its catalytic activity could represent a relevant strategy for the development of anti-coronavirus drugs. SARS-CoV-2 Mpro is a peculiar cysteine protease of the coronavirus family, responsible for the replication and infectivity of the parasite. This review offers a detailed analysis of the repurposed drugs and the newly synthesized molecules developed to date for the treatment of COVID-19 which share the common feature of targeting SARS-CoV-2 Mpro, as well as a brief overview of the main enzymatic and cell-based assays to efficaciously screen such compounds.
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Affiliation(s)
| | | | | | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy; (A.C.); (A.S.); (A.P.)
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Borch A, Kolster C, Gluud C, Gluud LL. Vaccines for preventing hepatitis B in healthcare workers (an updated protocol). THE COCHRANE DATABASE OF SYSTEMATIC REVIEWS 2017. [DOI: 10.1002/14651858.cd012695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anders Borch
- Copenhagen University Hospital Hvidovre; Gastrounit, Medical Division; Kettegård Alle 30, Hvidovre Denmark 2650
| | - Chastine Kolster
- Copenhagen University Hospital Hvidovre; Gastrounit, Medical Division; Kettegård Alle 30, Hvidovre Denmark 2650
| | - Christian Gluud
- Copenhagen Trial Unit, Centre for Clinical Intervention Research, Department 7812, Rigshospitalet, Copenhagen University Hospital; The Cochrane Hepato-Biliary Group; Blegdamsvej 9 Copenhagen Denmark DK-2100
| | - Lise Lotte Gluud
- Copenhagen University Hospital Hvidovre; Gastrounit, Medical Division; Kettegård Alle 30, Hvidovre Denmark 2650
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Abstract
Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become important and state of the art in the pharmaceutical industry. There has been an increasing awareness of the enormous potential of microorganisms and enzymes (biocatalysts) for the transformation of synthetic chemicals with high chemo-, regio- and enatioselectivities providing products in high yields and purity. In this article, biocatalytic processes are described for the synthesis of key chiral intermediates for development pharmaceuticals.
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Affiliation(s)
- Ramesh N Patel
- SLRP Associates, LLC, Consultation in Biocatalysis and Biotechnology, 572 Cabot Hill Road, Bridgewater, NJ 08807, USA.
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6
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Zhou WC, Zhang QB, Qiao L. Pathogenesis of liver cirrhosis. World J Gastroenterol 2014; 20:7312-7324. [PMID: 24966602 PMCID: PMC4064077 DOI: 10.3748/wjg.v20.i23.7312] [Citation(s) in RCA: 353] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/16/2014] [Accepted: 04/29/2014] [Indexed: 02/06/2023] Open
Abstract
Liver cirrhosis is the final pathological result of various chronic liver diseases, and fibrosis is the precursor of cirrhosis. Many types of cells, cytokines and miRNAs are involved in the initiation and progression of liver fibrosis and cirrhosis. Activation of hepatic stellate cells (HSCs) is a pivotal event in fibrosis. Defenestration and capillarization of liver sinusoidal endothelial cells are major contributing factors to hepatic dysfunction in liver cirrhosis. Activated Kupffer cells destroy hepatocytes and stimulate the activation of HSCs. Repeated cycles of apoptosis and regeneration of hepatocytes contribute to pathogenesis of cirrhosis. At the molecular level, many cytokines are involved in mediation of signaling pathways that regulate activation of HSCs and fibrogenesis. Recently, miRNAs as a post-transcriptional regulator have been found to play a key role in fibrosis and cirrhosis. Robust animal models of liver fibrosis and cirrhosis, as well as the recently identified critical cellular and molecular factors involved in the development of liver fibrosis and cirrhosis will facilitate the development of more effective therapeutic approaches for these conditions.
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Liu TL, Li W, Geng H, Wang CJ, Zhang X. Catalytic Enantioselective Desymmetrization of Meso Cyclic Anhydrides via Iridium-Catalyzed Hydrogenation. Org Lett 2013; 15:1740-3. [DOI: 10.1021/ol400533g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Tang-Lin Liu
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, China, and Department of Chemistry and Chemical Biology and Department of Pharmaceutical Chemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Wei Li
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, China, and Department of Chemistry and Chemical Biology and Department of Pharmaceutical Chemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Huiling Geng
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, China, and Department of Chemistry and Chemical Biology and Department of Pharmaceutical Chemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Chun-Jiang Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, China, and Department of Chemistry and Chemical Biology and Department of Pharmaceutical Chemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Xumu Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, China, and Department of Chemistry and Chemical Biology and Department of Pharmaceutical Chemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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Boceprevir: a protease inhibitor for the treatment of hepatitis C. Clin Ther 2012; 34:2021-38. [PMID: 22975763 DOI: 10.1016/j.clinthera.2012.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 08/17/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND Boceprevir is a protease inhibitor indicated for the treatment of chronic hepatitis C virus (HCV) genotype 1 infection in combination with peginterferon and ribavirin for treatment-naive patients and those who previously failed to improve with interferon and ribavirin treatment. OBJECTIVE This article provides an overview of the mechanism of action, pharmacologic and pharmacokinetic properties, clinical efficacy, and tolerability of boceprevir. METHODS Relevant information was identified through a search of PubMed (1990-July 2012), EMBASE (1990-July 2012), International Pharmaceutical Abstracts (1970-July 2012), and Google Scholar using the key words boceprevir, SCH 503034, non-structural protein 3 (NS3) serine protease inhibitor, and direct-acting antiviral agent (DAA). Additional information was obtained from the US Food and Drug Administration's Web site, review of the reference lists of identified articles, and posters and abstracts from scientific meetings. RESULTS Clinical efficacy of boceprevir was assessed in 2 Phase III trials, Serine Protease Inhibitor Therapy-2 (SPRINT-2) for treatment-naive patients and Retreatment with HCV Serine Protease Inhibitor Boceprevir and PegIntron/Rebetol 2 (RESPOND-2) for treatment-experienced patients. In SPRINT-2, patients were randomized to receive peginterferon + ribavirin (PR) or peginterferon + ribavirin + boceprevir (PRB); duration of boceprevir therapy varied from 24, 32, to 44 weeks on the basis of HCV RNA results. The primary endpoint was achievement of sustained virologic response (SVR; lower limit of detection, 9.3 IU/mL). The addition of boceprevir was shown to be superior, with overall SVR rates ranging from 63% to 66% compared with 38% with PR (P < 0.001). Results of SVR in SPRINT-2 were also reorganized to monitor SVRs in black and non-black patients. Treatment-experienced patients were assessed in RESPOND-2; however, null responders were excluded. Patients were again randomized to PR or PRB; duration of boceprevir therapy varied from 32 to 44 weeks on the basis of HCV RNA results. SVR was significantly higher in patients receiving boceprevir (59%-66% vs 21% with PR; P < 0.001). This benefit was seen in both previous nonresponders (SVR, 40%-52% vs 7% with PR), as well as previous relapsers (SVR, 69%-75% vs 29% with PR). Importantly, SVR could be attained with a shortened course of therapy in almost one half of all treated patients in SPRINT-2 (44%) and RESPOND-2 (46%). CONCLUSIONS Boceprevir was well tolerated in clinical trials and a welcomed addition to our HCV armamentarium.
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Patel RN. Biocatalysis: Synthesis of Key Intermediates for Development of Pharmaceuticals. ACS Catal 2011. [DOI: 10.1021/cs200219b] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ramesh N. Patel
- Biotechnology Department, Unimark Remedies, Ltd., Mumbai, India
- SLRP Associates, LLC, 572 Cabot Hill Road, Bridgewater, New Jersey 08807, United States
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Lu J, Zhou Y, Lin X, Jiang Y, Tian R, Zhang Y, Wu J, Zhang F, Zhang Y, Wang Y, Bi S. General epidemiological parameters of viral hepatitis A, B, C, and E in six regions of China: a cross-sectional study in 2007. PLoS One 2009; 4:e8467. [PMID: 20041146 PMCID: PMC2794385 DOI: 10.1371/journal.pone.0008467] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 12/03/2009] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Viral hepatitis is a serious health burden worldwide. To date, few reports have addressed the prevalence of hepatitis A, B, C, and E in China. Therefore, the general epidemiological parameters of viral hepatitis remain unknown. PRINCIPAL FINDINGS In this cross-sectional study, we performed a serological prevalence analysis of viral hepatitis A, B, C, and E in 8,762 randomly selected Chinese subjects, which represented six areas of China. The overall prevalence of anti-Hepatitis C virus antibody (anti-HCV) was 0.58%, which was much lower than was estimated by WHO. The prevalences of Hepatitis B virus surface antigen (HBsAg), anti-Hepatitis B virus surface protein antibody (HBsAb), and anti-Hepatitis B virus core protein antibody (HBcAb) were 5.84%, 41.31%, and 35.92%, respectively, whereas in the group of subjects less than 5 years old, these prevalences were 1.16%, 46.77%, and 8.69% respectively, which suggests that the Hepatitis B virus (HBV)-carrier population is decreasing, and the nationwide HBV vaccine program has contributed to the lowered HBV prevalence in the younger generation in China. Meanwhile, a large deficit remains in coverage provided by the national HBV immune program. In addition, our data suggested the possibility that HBsAb may not last long enough to protect people from HBV infection throughout life. The overall prevalence of anti-Hepatitis A virus antibody (anti-HAV) and anti-Hepatitis E virus antibody (anti-HEV) were as high as 72.87% and 17.66%, respectively. The indices increased with age, which suggests that a large proportion of Chinese adults are protected by latent infection. Furthermore, the pattern of HEV infection was significantly different among ethnic groups in China. CONCLUSIONS Our study provided much important information concerning hepatitis A, B, C, and E prevalence in China and will contribute to worldwide oversight of viral hepatitis.
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MESH Headings
- Adolescent
- Adult
- Biomarkers/blood
- Child
- Child, Preschool
- China/epidemiology
- Cross-Sectional Studies
- Female
- Geography
- Hepacivirus/immunology
- Hepatitis A/blood
- Hepatitis A/epidemiology
- Hepatitis A/immunology
- Hepatitis A/virology
- Hepatitis A Antibodies/immunology
- Hepatitis A Virus, Human/immunology
- Hepatitis B/blood
- Hepatitis B/epidemiology
- Hepatitis B/immunology
- Hepatitis B/virology
- Hepatitis B virus/immunology
- Hepatitis C/blood
- Hepatitis C/epidemiology
- Hepatitis C/immunology
- Hepatitis C/virology
- Hepatitis C Antibodies/immunology
- Hepatitis E/blood
- Hepatitis E/epidemiology
- Hepatitis E/immunology
- Hepatitis E/virology
- Hepatitis E virus/immunology
- Hepatitis, Viral, Human/blood
- Hepatitis, Viral, Human/epidemiology
- Hepatitis, Viral, Human/immunology
- Hepatitis, Viral, Human/virology
- Humans
- Male
- Middle Aged
- Prevalence
- Young Adult
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Affiliation(s)
- Jian Lu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Yongdong Zhou
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Xiaojing Lin
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Yongzhen Jiang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Ruiguang Tian
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Yonghui Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Jia Wu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Fengwei Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Yong Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Yue Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
| | - Shengli Bi
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Xuanwu District, Beijing, People's Republic of China
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Zhang JC, Nie QH. New antiviral choice for chronic hepatitis B: tenofovir disoproxil fumarate. Shijie Huaren Xiaohua Zazhi 2008; 16:2679-2688. [DOI: 10.11569/wcjd.v16.i24.2679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tenofovir disoproxil fumarate (TDF) is an oral prodrug of tenofovir, a novel, acyclic nucleotide analogue with in vitro activity against HIV-1 and HIV-2. TDF is licensed by American Food and Drug Administration (FDA) in 2001 for the treatment of HIV infection. TDF is currently one of the most widely used nucleotide reverse transcriptase inhibitors (NRTIs) for the treatment of HIV infection. Its efficacy, favorable toxicity profile, and convenient dosing have made this drug one of the most popular first-line treatment. Numerous studies have demonstrated the use of TDF in the treatment of HIV infection. It also has been shown to be effective in HIV/HBV coinfected patients and in patients with wild-type and lamivudine-resistant strains. Accumulating evidence suggests that TDF is more potent in suppressing HBV replication. In this review, we summarize the study progress of TDF in treating HBV infection.
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