1
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Li Q, Tavis JE. In Vitro Enzymatic and Cell Culture-Based Assays for Measuring Activity of HBV Ribonuclease H Inhibitors. Methods Mol Biol 2024; 2837:257-270. [PMID: 39044091 DOI: 10.1007/978-1-0716-4027-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
HBV is a small, enveloped DNA virus that replicates by reverse transcription of an RNA intermediate. Current anti-HBV treatment regiments employ interferon α or nucleos(t)ide analogs, but they are not curative, are of long duration, and can be accompanied by systemic side-effects. The HBV ribonuclease H (RNaseH) is essential for viral replication; however, it is unexploited as a drug target. RNaseH inhibitors that actively block viral replication would represent an important addition to the potential new drugs for treating HBV infection. Here, we describe two methods to measure the activity of RNaseH inhibitors. The DNA oligonucleotide-directed RNA cleavage assay allows mechanistic analysis of compounds for anti-HBV RNaseH activity. Analysis of preferential inhibition of plus-polarity DNA strand synthesis by HBV RNaseH inhibitors in a cell culture model of HBV replication can be used to measure the ability of RNaseH inhibitors to block viral replication.
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Affiliation(s)
- Qilan Li
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine and Saint Louis University Liver Center, Saint Louis, MO, USA
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine and Saint Louis University Liver Center, Saint Louis, MO, USA.
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2
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Woodson ME, Mottaleb MA, Murelli RP, Tavis JE. In vitro evaluation of tropolone absorption, metabolism, and clearance. Antiviral Res 2023; 220:105762. [PMID: 37996012 PMCID: PMC10843707 DOI: 10.1016/j.antiviral.2023.105762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Tropolone compounds can inhibit hepatitis B virus (HBV) replication at sub-micromolar levels and are synergistic upon co-treatment with nucleos(t)ide analog drugs. However, only a few compounds within this chemotype have been screened for their pharmacological properties. Here, we chose 36 structurally diverse tropolones from six subclasses to characterize their in vitro pharmacological parameters. All compounds were more soluble in pHs that reflect the gastrointestinal tract (pH 5 and 6.5) than plasma (pH 7.4). Those compounds that had solubility limits >100 μM were tested in a passive permeability assay, and there was no general trend in the compounds' passive permeability at any pH. Twenty-nine compounds with the best absorption parameters were tested in HEK293 cells to assess potential cytotoxicity; measured toxicities were similar to those in the hepatic HepDES19 cells used for screening (R2 = 0.55). Sixteen representative compounds were tested against five major CYP450 isoforms and there was no substantial inhibition by any compound against any of the enzymes tested (<50%). The t1/2 values of 15 compounds were determined in the microsome stability assay and 12 compounds were evaluated in plasma protein binding assays to assess factors affecting their rate of clearance. All compounds with detectable analyte peaks had t1/2 > 30 min, and while 4 of 12 had statistically significant decreased potency in conditions with increased albumin concentrations, only one compound's potency was biologically significant. These data indicate that the tropolones have pharmacological characteristics that reflect approved drugs and inform future structure activity relationships during drug design.
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Affiliation(s)
- Molly E Woodson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA; Institute for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, MO, USA
| | - M Abdul Mottaleb
- Institute for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, MO, USA
| | - Ryan P Murelli
- Department of Chemistry and Biochemistry, Brooklyn College, City University of New York, Brooklyn, NY, USA; The Graduate Center, City University of New York, New York, NY, USA
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA; Institute for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, MO, USA.
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3
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Moianos D, Prifti GM, Makri M, Zoidis G. Targeting Metalloenzymes: The "Achilles' Heel" of Viruses and Parasites. Pharmaceuticals (Basel) 2023; 16:901. [PMID: 37375848 DOI: 10.3390/ph16060901] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Metalloenzymes are central to the regulation of a wide range of essential viral and parasitic functions, including protein degradation, nucleic acid modification, and many others. Given the impact of infectious diseases on human health, inhibiting metalloenzymes offers an attractive approach to disease therapy. Metal-chelating agents have been expansively studied as antivirals and antiparasitics, resulting in important classes of metal-dependent enzyme inhibitors. This review provides the recent advances in targeting the metalloenzymes of viruses and parasites that impose a significant burden on global public health, including influenza A and B, hepatitis B and C, and human immunodeficiency viruses as well as Trypanosoma brucei and Trypanosoma cruzi.
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Affiliation(s)
- Dimitrios Moianos
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Georgia-Myrto Prifti
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Maria Makri
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
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4
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Kang JX, Zhao GK, Yang XM, Huang MX, Hui WQ, Zeng R, Ouyang Q. Recent advances on dual inhibitors targeting HIV reverse transcriptase associated polymerase and ribonuclease H. Eur J Med Chem 2023; 250:115196. [PMID: 36787657 DOI: 10.1016/j.ejmech.2023.115196] [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: 11/15/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Reverse transcriptase (RT) plays an indispensable role in the replication of human immunodeficiency virus (HIV) through its associated polymerase and ribonuclease H (RNase H) activities during the viral RNA genome transformation into proviral DNA. Due to the fact that HIV is a highly mutagenic virus and easily resistant to single-target RT inhibitors, dual inhibitors targeting HIV RT associated polymerase and RNase H have been developed. These dual inhibitors have the advantages of increasing efficacy, reducing drug resistance, drug-drug interactions, and cytotoxicity, as well as improving patient compliance. In this review, we summarize recent advances in polymerase/RNase H dual inhibitors focusing on drug design strategies, and structure-activity relationships and share new insights into developing anti-HIV drugs.
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Affiliation(s)
- Jia-Xiong Kang
- Department of Pharmacy, Armed Police Forces Hospital of Sichuan, 614000, Leshan, China
| | - Guang-Kuan Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Xiu-Ming Yang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Mou-Xin Huang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Wen-Qi Hui
- Department of Pharmacy, Xi'an Fifth Hospital, Xian, 710082, Shaanxi, China
| | - Rong Zeng
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Qin Ouyang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China.
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5
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Gazquez Casals A, Berkowitz AJ, Yu AJ, Waters HE, Schiavone DV, Kapkayeva DM, Morrison LA, Murelli RP. Antiviral activity of amide-appended α-hydroxytropolones against herpes simplex virus-1 and -2. RSC Adv 2023; 13:8743-8752. [PMID: 36936842 PMCID: PMC10016935 DOI: 10.1039/d2ra06749h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
α-Hydroxytropolones (αHTs) have potent antiviral activity against herpes simplex virus-1 and -2 (HSV-1 and HSV-2) in cell culture, including against acyclovir-resistant mutants, and as a result have the potential to be developed as antiviral drugs targeting these viruses. We recently described a convenient final-step amidation strategy to their synthesis, and this was used to generate 57 amide-substituted αHTs that were tested against hepatitis B virus. The following manuscript describes the evaluation of this library against HSV-1, as well as a subset against HSV-2. The structure-function analysis obtained from these studies demonstrates the importance of lipophilicity and rigidity to αHT-based anti-HSV potency, consistent with our prior work on smaller libraries. We used this information to synthesize and test a targeted library of 4 additional amide-appended αHTs. The most potent of this new series had a 50% effective concentration (EC50) for viral inhibition of 72 nM, on par with the most potent αHT antivirals we have found to date. Given the ease of synthesis of amide-appended αHTs, this new class of antiviral compounds and the chemistry to make them should be highly valuable in future anti-HSV drug development.
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Affiliation(s)
- Andreu Gazquez Casals
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Alex J Berkowitz
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
- PhD Program in Chemistry, The Graduate Center, The City University of New York New York NY USA
| | - Alice J Yu
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Hope E Waters
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Daniel V Schiavone
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
- PhD Program in Chemistry, The Graduate Center, The City University of New York New York NY USA
| | - Diana M Kapkayeva
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
| | - Lynda A Morrison
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
- PhD Program in Chemistry, The Graduate Center, The City University of New York New York NY USA
- PhD Program in Biochemistry, The Graduate Center, The City University of New York New York NY USA
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6
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Emerging Therapies for Chronic Hepatitis B and the Potential for a Functional Cure. Drugs 2023; 83:367-388. [PMID: 36906663 DOI: 10.1007/s40265-023-01843-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2023] [Indexed: 03/13/2023]
Abstract
Worldwide, an estimated 296 million people are living with chronic hepatitis B virus (HBV) infection, with a significant risk of morbidity and mortality. Current therapy with pegylated interferon (Peg-IFN) and indefinite or finite therapy with nucleoside/nucleotide analogues (Nucs) are effective in HBV suppression, hepatitis resolution, and prevention of disease progression. However, few achieve hepatitis B surface antigen (HBsAg) loss (functional cure), and relapse often occurs after the end of therapy (EOT) because these agents have no direct effect on durable template: covalently closed circular DNA (cccDNA) and integrated HBV DNA. Hepatitis B surface antigen loss rate increases slightly by adding or switching to Peg-IFN in Nuc-treated patients and this loss rate greatly increases up to 39% in 5 years with finite Nuc therapy with currently available Nuc(s). For this, great effort has been made to develop novel direct-acting antivirals (DAAs) and immunomodulators. Among the DAAs, entry inhibitors and capsid assembly modulators have little effect on reducing HBsAg levels; small interfering RNA, antisense oligonucleotides, and nucleic acid polymers in combination with Peg-IFN and Nuc may reduce HBsAg levels significantly, even a rate of HBsAg loss sustained for > 24 weeks after EOT up to 40%. Novel immunomodulators, including T-cell receptor agonists, check-point inhibitors, therapeutic vaccines, and monoclonal antibodies may restore HBV-specific T-cell response but not sustained HBsAg loss. The safety issues and the durability of HBsAg loss warrant further investigation. Combining agents of different classes has the potential to enhance HBsAg loss. Compounds directly targeting cccDNA would be more effective but are still in the early stage of development. More effort is required to achieve this goal.
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7
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Xie Z, Liang Z, Huang Y, Shi K, Zang N, Wang M, Liang T, Wei W. Discovery and biological evaluation of 2-((3-phenylisoxazol-5-yl) methoxy) benzamide derivatives as potent nucleocapsid inhibitors. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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8
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Tajwar R, Bradley DP, Ponzar NL, Tavis JE. Predicted structure of the hepatitis B virus polymerase reveals an ancient conserved protein fold. Protein Sci 2022; 31:e4421. [PMID: 36173165 PMCID: PMC9601786 DOI: 10.1002/pro.4421] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 11/12/2022]
Abstract
Hepatitis B virus (HBV) chronically infects >250 million people. It replicates by a unique protein-primed reverse transcription mechanism, and the primary anti-HBV drugs are nucleos(t)ide analogs targeting the viral polymerase (P). P has four domains compared to only two in most reverse transcriptases: the terminal protein (TP) that primes DNA synthesis, a spacer, the reverse transcriptase (RT), and the ribonuclease H (RNase H). Despite being a major drug target and catalyzing a reverse transcription pathway very different from the retroviruses, HBV P has resisted structural analysis for decades. Here, we exploited computational advances to model P. The TP wrapped around the RT domain rather than forming the anticipated globular domain, with the priming tyrosine poised over the RT active site. The orientation of the RT and RNase H domains resembled that of the retroviral enzymes despite the lack of sequences analogous to the retroviral linker region. The model was validated by mapping residues with known surface exposures, docking nucleic acids, mechanistically interpreting mutations with strong phenotypes, and docking inhibitors into the RT and RNase H active sites. The HBV P fold, including the orientation of the TP domain, was conserved among hepadnaviruses infecting rodent to fish hosts and a nackednavirus, but not in other non-retroviral RTs. Therefore, this protein fold has persisted since the hepadnaviruses diverged from nackednaviruses >400 million years ago. This model will advance mechanistic analyses into the poorly understood enzymology of HBV reverse transcription and will enable drug development against non-active site targets for the first time.
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Affiliation(s)
- Razia Tajwar
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
| | - Daniel P. Bradley
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
| | - Nathan L. Ponzar
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
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9
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Geerling E, Murphy V, Mai MC, Stone ET, Casals AG, Hassert M, O’Dea AT, Cao F, Donlin MJ, Elagawany M, Elgendy B, Pardali V, Giannakopoulou E, Zoidis G, Schiavone DV, Berkowitz AJ, Agyemang NB, Murelli RP, Tavis JE, Pinto AK, Brien JD. Metal coordinating inhibitors of Rift Valley fever virus replication. PLoS One 2022; 17:e0274266. [PMID: 36112605 PMCID: PMC9481026 DOI: 10.1371/journal.pone.0274266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a veterinary and human pathogen and is an agent of bioterrorism concern. Currently, RVFV treatment is limited to supportive care, so new drugs to control RVFV infection are urgently needed. RVFV is a member of the order Bunyavirales, whose replication depends on the enzymatic activity of the viral L protein. Screening for RVFV inhibitors among compounds with divalent cation-coordinating motifs similar to known viral nuclease inhibitors identified 47 novel RVFV inhibitors with selective indexes from 1.1–103 and 50% effective concentrations of 1.2–56 μM in Vero cells, primarily α-Hydroxytropolones and N-Hydroxypyridinediones. Inhibitor activity and selective index was validated in the human cell line A549. To evaluate specificity, select compounds were tested against a second Bunyavirus, La Crosse Virus (LACV), and the flavivirus Zika (ZIKV). These data indicate that the α-Hydroxytropolone and N-Hydroxypyridinedione chemotypes should be investigated in the future to determine their mechanism(s) of action allowing further development as therapeutics for RVFV and LACV, and these chemotypes should be evaluated for activity against related pathogens, including Hantaan virus, severe fever with thrombocytopenia syndrome virus, Crimean-Congo hemorrhagic fever virus.
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Affiliation(s)
- Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Valerie Murphy
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Maria C. Mai
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - E. Taylor Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Andreu Gazquez Casals
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Mariah Hassert
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Austin T. O’Dea
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Feng Cao
- John Cochran Division, Department of Veterans Affairs Medical Center, Saint Louis, Missouri, United States of America
| | - Maureen J. Donlin
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Mohamed Elagawany
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, Saint Louis, Missouri, United States of America
| | - Bahaa Elgendy
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, Saint Louis, Missouri, United States of America
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, Saint Louis, Missouri, United States of America
| | - Vasiliki Pardali
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Erofili Giannakopoulou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Daniel V. Schiavone
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - Alex J. Berkowitz
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - Nana B. Agyemang
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - Ryan P. Murelli
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail:
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10
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Cao M, Yuan D, Jiang H, Zhou G, Chen C, Han G. Long non-coding RNA WAC antisense RNA 1 mediates hepatitis B virus replication <em>in vitro</em> by reinforcing miR-192-5p/ATG7-induced autophagy. Eur J Histochem 2022; 66. [PMID: 36053263 PMCID: PMC9471915 DOI: 10.4081/ejh.2022.3438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNA WAC antisense RNA 1 (lncRNA WAC-AS1) is involved in the replication of the hepatitis B virus (HBV). The purpose of this study was to determine its functions and specific mechanism. The levels of lncRNA WAC-AS1, RNA (miR)-192-5p and were examined in serum of HBV-infected patients and in HepG2.2.15 cells using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and Western blotting. Using the database starBase, the target binding sites of lncRNA WAC-AS1 and miR-192-5p were predicted and confirmed by dual-luciferase reporter assay and RNA pull-down assay. The expression of pgRNA and HBV DNA was determined by qRT-PCR, while the levels of HBeAg and HBsAg were measured by enzyme-linked immunosorbent assay (ELISA). Using laser scanning confocal microscopy, the light chain 3 (LC3) expression was analyzed. qRT-PCR and Western blotting were used to assess the expression of beclin-1, p62, and LC3I/II. Overexpression of lncRNA WAC-AS1, upregulation of ATG7. and downregulation of miR-192-5p were observed in the serum of HBV-infected patients and the in vitro model. miR-192-5p directly targets lncRNA WAC-AS1. LncRNA WAC-AS1 was downregulated in lncRNA WAC-AS1-shRNA‒transfected cells. miR-192-5p was upregulated in lncRNA WAC-AS1-shRNA-transfected cells and downregulated in cells transfected with a miR-192-5p inhibitor. In HepG2 2.15 cells, the downregulation of lncRNA WAC-AS1 inhibited HBV replication and autophagy. In contrast, the miR-192-5p inhibitor-transfected group exhibited the opposite results, and ATG7 overexpression reversed the effects of miR-192-5p mimic or lncRNA WAC-AS1-shRNA on HBV replication and cell autophagy. Our findings indicate that lncRNA WAC-AS1 regulates HBV replication by reinforcing the autophagy induced by miR-192-5p/ATG7. Consequently, lncRNA WAC-AS1 may serve as a therapeutically-promising target in HBV patients.
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Affiliation(s)
- Minkai Cao
- Department of Obstetrics and Gynecology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing.
| | - Deping Yuan
- Department of Obstetrics and Gynecology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing.
| | - Hongxiu Jiang
- Department of Obstetrics and Gynecology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing.
| | - Guanlun Zhou
- Department of Obstetrics and Gynecology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing.
| | - Chao Chen
- Department of Obstetrics and Gynecology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing.
| | - Guorong Han
- Department of Obstetrics and Gynecology, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing.
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11
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Patel N, Abulwerdi F, Fatehi F, Manfield IW, Le Grice S, Schneekloth JS, Twarock R, Stockley PG. Dysregulation of Hepatitis B Virus Nucleocapsid Assembly in vitro by RNA-binding Small Ligands. J Mol Biol 2022; 434:167557. [PMID: 35341740 PMCID: PMC7612645 DOI: 10.1016/j.jmb.2022.167557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 12/12/2022]
Abstract
RNA sequences/motifs dispersed across the genome of Hepatitis B Virus regulate formation of nucleocapsid-like particles (NCPs) by core protein (Cp) in vitro, in an epsilon/polymerase-independent fashion. These multiple RNA Packaging Signals (PSs) can each form stem-loops encompassing a Cp-recognition motif, -RGAG-, in their loops. Drug-like molecules that bind the most important of these PS sites for NCP assembly regulation with nanomolar affinities, were identified by screening an immobilized ligand library with a fluorescently-labelled, RNA oligonucleotide encompassing this sequence. Sixty-six of these "hits", with affinities ranging from low nanomolar to high micromolar, were purchased as non-immobilized versions. Their affinities for PSs and effects on NCP assembly were determined in vitro by Surface Plasmon Resonance. High-affinity ligand binding is dependent on the presence of an -RGAG- motif within the loop of the PS, consistent with ligand cross-binding between PS sites. Simple structure-activity relationships show that it is also dependent on the presence of specific functional groups in these ligands. Some compounds are potent inhibitors of in vitro NCP assembly at nanomolar concentrations. Despite appropriate logP values, these ligands do not inhibit HBV replication in cell culture. However, modelling confirms the potential of using PS-binding ligands to target NCP assembly as a novel anti-viral strategy. This also allows for computational exploration of potential synergic effects between anti-viral ligands directed at distinct molecular targets in vivo. HBV PS-regulated assembly can be dysregulated by novel small molecule RNA-binding ligands opening a novel target for developing directly-acting anti-virals against this major pathogen.
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Affiliation(s)
- Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. https://twitter.com/FBSResearch
| | - Fardokht Abulwerdi
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, YO10 5DD, UK; York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stuart Le Grice
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - John S Schneekloth
- Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, United States
| | - Reidun Twarock
- Department of Mathematics, University of York, York, YO10 5DD, UK; York Cross-disciplinary Centre for Systems Analysis, University of York, York, YO10 5GE, UK; Department of Biology, University of York, York, YO10 5DD, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. https://twitter.com/AstburyCentre
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12
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Alpha-hydroxytropolones are noncompetitive inhibitors of human RNase H1 that bind to the active site and modulate substrate binding. J Biol Chem 2022; 298:101790. [PMID: 35247386 PMCID: PMC9034292 DOI: 10.1016/j.jbc.2022.101790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 11/23/2022] Open
Abstract
The ribonucleases H (RNases H) of HIV and hepatitis B virus are type 1 RNases H that are promising drug targets because inhibiting their activity blocks viral replication. Eukaryotic ribonuclease H1 (RNase H1) is an essential protein and a probable off-target enzyme for viral RNase H inhibitors. α-hydroxytropolones (αHTs) are a class of anti-RNase H inhibitors that can inhibit the HIV, hepatitis B virus, and human RNases H1; however, it is unclear how these inhibitors could be developed to distinguish between these enzymes. To accelerate the development of selective RNase H inhibitors, we performed biochemical and kinetic studies on the human enzyme, which was recombinantly expressed in Escherichia coli. Size-exclusion chromatography showed that free RNase H1 is monomeric and forms a 2:1 complex with a substrate of 12 bp. FRET heteroduplex cleavage assays were used to test inhibition of RNase H1 in steady-state kinetics by two structurally diverse αHTs, 110 and 404. We determined that turnover rate was reduced, but inhibition was not competitive with substrate, despite inhibitor binding to the active site. Given the compounds’ reversible binding to the active site, we concluded that traditional noncompetitive and mixed inhibition mechanisms are unlikely. Instead, we propose a model in which, by binding to the active site, αHTs stabilize an inactive enzyme–substrate–inhibitor complex. This new model clarifies the mechanism of action of αHTs against RNase H1 and will aid the development of RNase H inhibitors selective for the viral enzymes.
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Bradley DP, O’Dea AT, Woodson ME, Li Q, Ponzar NL, Knier A, Rogers BL, Murelli RP, Tavis JE. Effects of Troponoids on Mitochondrial Function and Cytotoxicity. Antimicrob Agents Chemother 2022; 66:e0161721. [PMID: 34694883 PMCID: PMC8765277 DOI: 10.1128/aac.01617-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
The α-hydroxytropolones (αHTs) are troponoid inhibitors of hepatitis B virus (HBV) replication that can target HBV RNase H with submicromolar efficacies. αHTs and related troponoids (tropones and tropolones) can be cytotoxic in cell lines as measured by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assays that assess mitochondrial function. Previous studies suggest that tropolones induce cytotoxicity through inhibition of mitochondrial respiration. Therefore, we screened 35 diverse troponoids for effects on mitochondrial function, mitochondrial/nuclear genome ratios, cytotoxicity, and reactive oxygen species (ROS) production. Troponoids as a class did not inhibit respiration or glycolysis, although the α-ketotropolone subclass interfered with these processes. The troponoids had no impact on the mitochondrial DNA/nuclear DNA ratio after 3 days of compound exposure. The patterns of troponoid-induced cytotoxicity among three hepatic cell lines were similar for all compounds, but three potent HBV RNase H inhibitors were not cytotoxic in primary human hepatocytes. Tropolones and αHTs increased ROS production in cells at cytotoxic concentrations but had no effect at lower concentrations that efficiently inhibit HBV replication. Troponoid-mediated cytotoxicity was significantly decreased upon the addition of the ROS scavenger N-acetylcysteine. These studies show that troponoids can increase ROS production at high concentrations within cell lines, leading to cytotoxicity, but are not cytotoxic in primary hepatocytes. Future development of αHTs as potential therapeutics against HBV may need to mitigate ROS production by altering compound design and/or by coadministering ROS antagonists to ameliorate increased ROS levels.
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Affiliation(s)
- Daniel P. Bradley
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri, USA
| | - Austin T. O’Dea
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Molly E. Woodson
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri, USA
| | - Qilan Li
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri, USA
| | - Nathan L. Ponzar
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri, USA
| | - Alaina Knier
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri, USA
| | | | - Ryan P. Murelli
- Brooklyn College, City University of New York, New York, New York, USA
- Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, New York, USA
| | - John E. Tavis
- Saint Louis University School of Medicine, St. Louis, Missouri, USA
- Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri, USA
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Berkowitz AJ, Murelli RP. Synthesis of α-Tropolones through Autoxidation of Dioxole-Fused Cycloheptatrienes. J Org Chem 2022; 87:4499-4507. [PMID: 35007070 PMCID: PMC9002940 DOI: 10.1021/acs.joc.1c02713] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we describe the formation of tropolones through the autoxidation of Büchner reaction-derived cycloheptatrienes. The reaction is exceptionally simple procedurally, as it involves blowing a stream of compressed air over the cycloheptatriene, and the products can be obtained without any need for chromatography. The chemistry works specifically on dioxolane-fused systems or close variants, and substitution patterns are also important. A radical-based mechanistic hypothesis is put forward to explain these results. Finally, we demonstrate the utility of the overall process in the synthesis of amide-appended tropolones and an isomer of stipitatic acid.
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Affiliation(s)
- Alex J Berkowitz
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, New York 11210, United States.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, New York 11210, United States.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States
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15
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Abstract
Hepatitis B virus (HBV) is a hepatotropic, partially double-stranded DNA virus that replicates by reverse transcription and is a major cause of chronic liver disease and hepatocellular carcinoma. Reverse transcription is catalyzed by the four-domain multifunctional HBV polymerase (P) protein that has protein-priming, RNA- and DNA-dependent DNA synthesis (i.e., reverse transcriptase), and ribonuclease H activities. P also likely promotes the three strand transfers that occur during reverse transcription, and it may participate in immune evasion by HBV. Reverse transcription is primed by a tyrosine residue in the amino-terminal domain of P, and P remains covalently attached to the product DNA throughout reverse transcription. The reverse transcriptase activity of P is the target for the nucleos(t)ide analog drugs that dominate HBV treatment, and P is the target of ongoing efforts to develop new drugs against both the reverse transcriptase and ribonuclease H activities. Despite the unusual reverse transcription pathway catalyzed by P and the importance of P to HBV therapy, understanding the enzymology and structure of HBV P severely lags that of the retroviral reverse transcriptases due to substantial technical challenges to studying the enzyme. Obtaining a better understanding of P will broaden our appreciation of the diversity among reverse transcribing elements in nature, and will help improve treatment for people chronically infected with HBV.
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Affiliation(s)
- Daniel N Clark
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Razia Tajwar
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States
| | - Jianming Hu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States.
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Efficient Inhibition of Hepatitis B Virus (HBV) Replication and cccDNA Formation by HBV Ribonuclease H Inhibitors during Infection. Antimicrob Agents Chemother 2021; 65:e0146021. [PMID: 34516242 DOI: 10.1128/aac.01460-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The hepatitis B virus (HBV) ribonuclease H (RNase H) is an attractive but unexploited drug target. Here, we addressed three limitations to the current state of RNase H inhibitor development: (a) Efficacy has been assessed only in transfected cell lines. (b) Cytotoxicity data are from transformed cell lines rather than primary cells. (c) It is unknown how the compounds work against nucleos(t)ide analog resistant HBV strains. Three RNase H inhibitors from different chemotypes, 110 (α-hydroxytropolone), 1133 (N-hydroxypyridinedione), and 1073 (N-hydroxynapthyridinone), were tested in HBV-infected HepG2-NTCP cells for inhibition of cccDNA accumulation and HBV product formation. 50% effective concentrations (EC50s) were 0.049-0.078 μM in the infection studies compared to 0.29-1.6 μM in transfected cells. All compounds suppressed cccDNA formation by >98% at 5 μM when added shortly after infection. HBV RNA, intracellular and extracellular DNA, and HBsAg secretion were all robustly suppressed. The greater efficacy of the inhibitors when added shortly after infection is presumably due to blocking amplification of the HBV cccDNA, which suppresses events downstream of cccDNA formation. The compounds had 50% cytotoxic concentrations (CC50s) of 16-100 μM in HepG2-derived cell lines but were nontoxic in primary human hepatocytes, possibly due to the quiescent state of the hepatocytes. The compounds had similar EC50s against replication of wild-type, lamivudine-resistant, and adefovir/lamivudine-resistant HBV, as expected because the RNase H inhibitors do not target the viral reverse transcriptase active site. These studies expand confidence in inhibiting the HBV RNase H as a drug strategy and support inclusion of RNase H inhibitors in novel curative drug combinations for HBV.
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Prifti GM, Moianos D, Giannakopoulou E, Pardali V, Tavis JE, Zoidis G. Recent Advances in Hepatitis B Treatment. Pharmaceuticals (Basel) 2021; 14:417. [PMID: 34062711 PMCID: PMC8147224 DOI: 10.3390/ph14050417] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/10/2023] Open
Abstract
Hepatitis B virus infection affects over 250 million chronic carriers, causing more than 800,000 deaths annually, although a safe and effective vaccine is available. Currently used antiviral agents, pegylated interferon and nucleos(t)ide analogues, have major drawbacks and fail to completely eradicate the virus from infected cells. Thus, achieving a "functional cure" of the infection remains a real challenge. Recent findings concerning the viral replication cycle have led to development of novel therapeutic approaches including viral entry inhibitors, epigenetic control of cccDNA, immune modulators, RNA interference techniques, ribonuclease H inhibitors, and capsid assembly modulators. Promising preclinical results have been obtained, and the leading molecules under development have entered clinical evaluation. This review summarizes the key steps of the HBV life cycle, examines the currently approved anti-HBV drugs, and analyzes novel HBV treatment regimens.
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Affiliation(s)
- Georgia-Myrto Prifti
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - Dimitrios Moianos
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - Erofili Giannakopoulou
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - Vasiliki Pardali
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - John E. Tavis
- Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO 63104, USA;
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
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Bassit L, Ono SK, Schinazi RF. Moving Fast Toward Hepatitis B Virus Elimination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:115-138. [PMID: 34258739 DOI: 10.1007/978-981-16-0267-2_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Currently, there are two safe and effective therapeutic strategies for chronic hepatitis B treatment, namely, nucleoside analogs and interferon alpha (pegylated or non-pegylated). These treatments can control viral replication and improve survival; however, they do not eliminate the virus and therefore require long-term continued therapy. In addition, there are significant concerns about virus rebound on discontinuation of therapy and the development of fibrosis and hepatocellular carcinoma despite therapy. Therefore, the search for new, more effective, and safer antiviral agents that can cure hepatitis B virus (HBV) continues. Anti-HBV drug discovery and development is fundamentally impacted by our current understanding of HBV replication, disease physiopathology, and persistence of HBV covalently closed circular DNA (cccDNA). Several HBV replication targets are the basis for novel anti-HBV drug development strategies. Many of them are already in clinical trial phase 1 or 2, while others with promising results are still in preclinical stages. As research intensifies, potential HBV curative therapies and modalities in the pipeline are now on the horizon.
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Affiliation(s)
- Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Suzane Kioko Ono
- Department of Gastroenterology, University of Sao Paulo School of Medicine, Sao Paulo, SP, Brazil
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, USA.
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Molecular, Evolutionary, and Structural Analysis of the Terminal Protein Domain of Hepatitis B Virus Polymerase, a Potential Drug Target. Viruses 2020; 12:v12050570. [PMID: 32455999 PMCID: PMC7291194 DOI: 10.3390/v12050570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022] Open
Abstract
Approximately 250 million people are living with chronic hepatitis B virus (HBV) infections, which claim nearly a million lives annually. The target of all current HBV drug therapies (except interferon) is the viral polymerase; specifically, the reverse transcriptase domain. Although no high-resolution structure exists for the HBV polymerase, several recent advances have helped to map its functions to specific domains. The terminal protein (TP) domain, unique to hepadnaviruses such as HBV, has been implicated in the binding and packaging of the viral RNA, as well as the initial priming of and downstream synthesis of viral DNA—all of which make the TP domain an attractive novel drug target. This review encompasses three types of analysis: sequence conservation analysis, secondary structure prediction, and the results from mutational studies. It is concluded that the TP domain of HBV polymerase is comprised of seven subdomains (three unstructured loops and four helical regions) and that all three loop subdomains and Helix 5 are the major determinants of HBV function within the TP domain. Further studies, such as modeling inhibitors of these critical TP subdomains, will advance the TP domain of HBV polymerase as a therapeutic drug target in the progression towards a cure.
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