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Giannakopoulou E, Akrani I, Mpekoulis G, Frakolaki E, Dimitriou M, Myrianthopoulos V, Vassilaki N, Zoidis G. Novel Pyrazino[1,2- a]indole-1,3(2 H,4 H)-dione Derivatives Targeting the Replication of Flaviviridae Viruses: Structural and Mechanistic Insights. Viruses 2024; 16:1238. [PMID: 39205212 PMCID: PMC11360281 DOI: 10.3390/v16081238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Infections with Flaviviridae viruses, such as hepatitis C (HCV), dengue (DENV), and yellow fever (YFV) viruses, are major public health problems worldwide. In the case of HCV, treatment is associated with drug resistance and high costs, while there is no clinically approved therapy for DENV and YFV. Consequently, there is still a need for new chemotherapies with alternative modes of action. We have previously identified novel 2-hydroxypyrazino[1,2-a]indole-1,3(2H,4H)-diones as metal-chelating inhibitors targeting HCV RNA replication. Here, by utilizing a structure-based approach, we rationally designed a second series of compounds by introducing various substituents at the indole core structure and at the imidic nitrogen, to improve specificity against the RNA-dependent RNA polymerase (RdRp). The resulting derivatives were evaluated for their potency against HCV genotype 1b, DENV2, and YFV-17D using stable replicon cell lines. The most favorable substitution was nitro at position 6 of the indole ring (compound 36), conferring EC50 1.6 μM against HCV 1b and 2.57 μΜ against HCV 1a, with a high selectivity index. Compound 52, carrying the acetohydroxamic acid functionality (-CH2CONHOH) on the imidic nitrogen, and compound 78, the methyl-substituted molecule at the position 4 indolediketopiperazine counterpart, were the most effective against DENV and YFV, respectively. Interestingly, compound 36 had a high genetic barrier to resistance and only one resistance mutation was detected, T181I in NS5B, suggesting that the compound target HCV RdRp is in accordance with our predicted model.
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Affiliation(s)
- Erofili Giannakopoulou
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - Ifigeneia Akrani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - George Mpekoulis
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Marios Dimitriou
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Vassilios Myrianthopoulos
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Grigoris Zoidis
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
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2
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Moianos D, Makri M, Prifti GM, Chiotellis A, Pappas A, Woodson ME, Tajwar R, Tavis JE, Zoidis G. N-Hydroxypiridinedione: A Privileged Heterocycle for Targeting the HBV RNase H. Molecules 2024; 29:2942. [PMID: 38931006 PMCID: PMC11206691 DOI: 10.3390/molecules29122942] [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: 05/29/2024] [Revised: 06/12/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Hepatitis B virus (HBV) remains a global health threat. Ribonuclease H (RNase H), part of the virus polymerase protein, cleaves the pgRNA template during viral genome replication. Inhibition of RNase H activity prevents (+) DNA strand synthesis and results in the accumulation of non-functional genomes, terminating the viral replication cycle. RNase H, though promising, remains an under-explored drug target against HBV. We previously reported the identification of a series of N-hydroxypyridinedione (HPD) imines that effectively inhibit the HBV RNase H. In our effort to further explore the HPD scaffold, we designed, synthesized, and evaluated 18 novel HPD oximes, as well as 4 structurally related minoxidil derivatives and 2 barbituric acid counterparts. The new analogs were docked on the RNase H active site and all proved able to coordinate the two Mg2+ ions in the catalytic site. All of the new HPDs effectively inhibited the viral replication in cell assays exhibiting EC50 values in the low μM range (1.1-7.7 μM) with low cytotoxicity, resulting in selectivity indexes (SI) of up to 92, one of the highest reported to date among HBV RNase H inhibitors. Our findings expand the structure-activity relationships on the HPD scaffold, facilitating the development of even more potent anti-HBV agents.
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Affiliation(s)
- Dimitrios Moianos
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
| | - Maria Makri
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
| | - Georgia-Myrto Prifti
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
| | - Aristeidis Chiotellis
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Center for Scientific Research “Demokritos”, 15310 Athens, Greece; (A.C.); (A.P.)
| | - Alexandros Pappas
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Center for Scientific Research “Demokritos”, 15310 Athens, Greece; (A.C.); (A.P.)
| | - Molly E. Woodson
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA; (M.E.W.); (R.T.); (J.E.T.)
| | - Razia Tajwar
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA; (M.E.W.); (R.T.); (J.E.T.)
| | - John E. Tavis
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA; (M.E.W.); (R.T.); (J.E.T.)
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
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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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Jin Y, Wang S, Xu S, Zhao S, Xu X, Poongavanam V, Menéndez-Arias L, Zhan P, Liu X. Targeting hepatitis B virus cccDNA levels: recent progress in seeking small molecule drug candidates. Drug Discov Today 2023; 28:103617. [PMID: 37196762 DOI: 10.1016/j.drudis.2023.103617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Hepatitis B virus (HBV) infection is a major global health problem that puts people at high risk of death from cirrhosis and liver cancer. The presence of covalently closed circular DNA (cccDNA) in infected cells is considered to be the main obstacle to curing chronic hepatitis B. At present, the cccDNA cannot be completely eliminated by standard treatments. There is an urgent need to develop drugs or therapies that can reduce HBV cccDNA levels in infected cells. We summarize the discovery and optimization of small molecules that target cccDNA synthesis and degradation. These compounds are cccDNA synthesis inhibitors, cccDNA reducers, core protein allosteric modulators, ribonuclease H inhibitors, cccDNA transcriptional modulators, HBx inhibitors and other small molecules that reduce cccDNA levels. Teaser: HBV covalently closed circular DNA (cccDNA) can be stably maintained in infected cells for a prolonged period, and this is the fundamental reason why hepatitis B cannot be completely cured. Here, we review recent progress in the development of small molecules that can reduce cccDNA levels in infected cells.
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Affiliation(s)
- Yu Jin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shuo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xiangrui Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), 28049 Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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5
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Ranga A, Gupta A, Yadav L, Kumar S, Jain P. Advancing beyond reverse transcriptase inhibitors: The new era of hepatitis B polymerase inhibitors. Eur J Med Chem 2023; 257:115455. [PMID: 37216809 DOI: 10.1016/j.ejmech.2023.115455] [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: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Hepatitis B virus (HBV) is a genetically diverse blood-borne virus responsible for chronic hepatitis B. The HBV polymerase plays a key role in viral genome replication within the human body and has been identified as a potential drug target for chronic hepatitis B therapeutics. However, available nucleotide reverse transcriptase inhibitors only target the reverse transcriptase domain of the HBV polymerase; they also pose resistance issues and require lifelong treatment that can burden patients financially. In this study, various chemical classes are reviewed that have been developed to target different domains of the HBV polymerase: Terminal protein, which plays a vital role in the formation of the viral DNA; Reverse transcriptase, which is responsible for the synthesis of the viral DNA from RNA, and; Ribonuclease H, which is responsible for degrading the RNA strand in the RNA-DNA duplex formed during the reverse transcription process. Host factors that interact with the HBV polymerase to achieve HBV replication are also reviewed; these host factors can be targeted by inhibitors to indirectly inhibit polymerase functionality. A detailed analysis of the scope and limitations of these inhibitors from a medicinal chemistry perspective is provided. The structure-activity relationship of these inhibitors and the factors that may affect their potency and selectivity are also examined. This analysis will be useful in supporting the further development of these inhibitors and in designing new inhibitors that can inhibit HBV replication more efficiently.
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Affiliation(s)
- Abhishek Ranga
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Aarti Gupta
- Department of Pharmaceutical Biotechnology, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Laxmi Yadav
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
| | - Priti Jain
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
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6
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Pan Y, Xia H, He Y, Zeng S, Shen Z, Huang W. The progress of molecules and strategies for the treatment of HBV infection. Front Cell Infect Microbiol 2023; 13:1128807. [PMID: 37009498 PMCID: PMC10053227 DOI: 10.3389/fcimb.2023.1128807] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023] Open
Abstract
Hepatitis B virus infections have always been associated with high levels of mortality. In 2019, hepatitis B virus (HBV)-related diseases resulted in approximately 555,000 deaths globally. In view of its high lethality, the treatment of HBV infections has always presented a huge challenge. The World Health Organization (WHO) came up with ambitious targets for the elimination of hepatitis B as a major public health threat by 2030. To accomplish this goal, one of the WHO's strategies is to develop curative treatments for HBV infections. Current treatments in a clinical setting included 1 year of pegylated interferon alpha (PEG-IFNα) and long-term nucleoside analogues (NAs). Although both treatments have demonstrated outstanding antiviral effects, it has been difficult to develop a cure for HBV. The reason for this is that covalently closed circular DNA (cccDNA), integrated HBV DNA, the high viral burden, and the impaired host immune responses all hinder the development of a cure for HBV. To overcome these problems, there are clinical trials on a number of antiviral molecules being carried out, all -showing promising results so far. In this review, we summarize the functions and mechanisms of action of various synthetic molecules, natural products, traditional Chinese herbal medicines, as clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR/Cas)-based systems, zinc finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), all of which could destroy the stability of the HBV life cycle. In addition, we discuss the functions of immune modulators, which can enhance or activate the host immune system, as well some representative natural products with anti-HBV effects.
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Affiliation(s)
| | | | | | | | | | - Wenhai Huang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, China
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7
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Wang Z, Geraghty RJ. Viral Nucleases. Viruses 2023; 15:740. [PMID: 36992449 PMCID: PMC10052875 DOI: 10.3390/v15030740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
Nucleases are ubiquitous hydrolytic enzymes that cleave phosphodiester bond of DNA (DNases), RNA (RNases), or protein-RNA/DNA (phosphodiesterases), within the strand (endonucleases) or from the end (exonucleases) [...].
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Affiliation(s)
- Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J. Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
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8
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Schiavone DV, Kapkayeva DM, Li Q, Woodson ME, Casals AG, Morrison LA, Tavis JE, Murelli RP. Synthesis of Polyoxygenated Tropolones and their Antiviral Activity against Hepatitis B Virus and Herpes Simplex Virus-1. Chemistry 2022; 28:e202104112. [PMID: 34984767 PMCID: PMC8858858 DOI: 10.1002/chem.202104112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 11/06/2022]
Abstract
Polyoxygenated tropolones possess a broad range of biological activity, and as a result are promising lead structures or fragments for drug development. However, structure-function studies and subsequent optimization have been challenging, in part due to the limited number of readily available tropolones and the obstacles to their synthesis. Oxidopyrylium [5+2] cycloaddition can effectively generate a diverse array of seven-membered ring carbocycles, and as a result can provide a highly general strategy for tropolone synthesis. Here, we describe the use of 3-hydroxy-4-pyrone-based oxidopyrylium cycloaddition chemistry in the synthesis of functionalized 3,7-dimethoxytropolones, 3,7-dihydroxytropolones, and isomeric 3-hydroxy-7-methoxytropolones through complementary benzyl alcohol-incorporating procedures. The antiviral activity of these molecules against herpes simplex virus-1 and hepatitis B virus is also described, highlighting the value of this approach and providing new structure-function insights relevant to their antiviral activity.
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Affiliation(s)
- Daniel V. Schiavone
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - Diana M. Kapkayeva
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA
| | - Qilan Li
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
| | - Molly E. Woodson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
| | - Andreu Gazquez Casals
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
| | - Lynda A. Morrison
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
| | - Ryan P. Murelli
- Department of Chemistry, Brooklyn College of the City University of New York, Brooklyn, New York 11210, USA,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
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9
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Akbar SMF, Al Mahtab M, Cesar Aguilar J, Uddin MH, Khan MSI, Yoshida O, Penton E, Gerardo GN, Hiasa Y. Exploring evidence-based innovative therapy for the treatment of chronic HBV infection: experimental and clinical. EXPLORATION OF MEDICINE 2021. [DOI: 10.37349/emed.2021.00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
With the advent of various vaccines and antimicrobial agents during the 20th century, the control and containment of infectious diseases appeared to be a matter of time. However, studies unveiled the diverse natures of microbes, their lifestyle, and pathogenetic potentials. Since the ground-breaking discovery of the hepatitis B virus (HBV) by Baruch Blumberg and the subsequent development of a vaccine in the early 1980s, the main task of the scientific community has been to develop a proper management strategy for HBV-induced chronic liver diseases. In the early 1980’s, standard interferon (IFN) induced a reduction of HBV DNA levels, followed by the normalization of serum transaminases (alanine aminotransferase, ALT), in some chronic hepatitis B (CHB) patients. However, in the course of time, the limitations of standard IFN became evident, and the search for an alternative began. In the late 1980’s, nucleoside analogs entered the arena of CHB treatment as oral drugs with potent antiviral capacities. At the beginning of the 21st century, insights were developed into the scope and limitations of standard IFN, pegylated-IFN as well as nucleoside analogs for treating CHB. Considering the non-cytopathic nature of the HBV, the presence of covalently closed circular DNA (cccDNA) in the nucleus of the infected hepatocytes and HBV-induced immune-mediated liver damages, a new field of CHB management was initiated by modulating the hosts’ immune system through immune therapy. This review will discuss the nature and design of innovative immune therapy for CHB.
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Affiliation(s)
- Sheikh Mohammad Fazle Akbar
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Ehime 7910295, Japan
| | - Mamun Al Mahtab
- Department of Hepatology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka 1000, Bangladesh
| | - Julio Cesar Aguilar
- Center for Genetic Engineering and Biotechnology, Havana, Havana 10600, Cuba
| | | | - Md. Sakirul Islam Khan
- Department of Anatomy and Embryology, Ehime University Graduate School of Medicine, Ehime 7910295, Japan
| | - Osamu Yoshida
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Ehime 7910295, Japan
| | - Eduardo Penton
- Center for Genetic Engineering and Biotechnology, Havana, Havana 10600, Cuba
| | | | - Yoichi Hiasa
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Ehime 7910295, Japan
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10
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021; 17:e1009384. [PMID: 34516563 PMCID: PMC8478224 DOI: 10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 09/28/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2. The on-going coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is significantly affecting the world health. Unfortunately, over 180 million cases of COVID-19 resulting in nearly 4 million deaths have been reported till June, 2021. In this study, using a combination of bioinformatics, biochemical and mass spectrometry methods, we show that the Nidovirus RdRp associated Nucleotidyl transferase (NiRAN) domain of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 exhibits a kinase like activity. Additionally, we also show that few broad spectrum anti-cancer and anti-microbial drugs dampen this kinase like activity. Of note, Sorafenib, an FDA approved anti-cancer kinase inhibiting drug significantly reduces the SARS-CoV-2 load in cell lines. Our study suggests that NiRAN domain of the SARS-CoV-2 RdRp is indispensible for the successful viral life cycle and shows that abolishing this enzymatic function of RdRp by small molecule inhibitors may open novel avenues for COVID-19 therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Tanmay Majumdar
- National Institute of Immunology, New Delhi, India
- * E-mail: (TM); (JJ); (BKB)
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Tamil Nadu, India
- * E-mail: (TM); (JJ); (BKB)
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11
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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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12
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Lin J, Zangi M, Kumar TVH, Shakar Reddy M, Reddy LVR, Sadhukhan SK, Bradley DP, Moreira-Walsh B, Edwards TC, O’Dea AT, Tavis JE, Meyers MJ, Donlin MJ. Synthetic Derivatives of Ciclopirox are Effective Inhibitors of Cryptococcus neoformans. ACS OMEGA 2021; 6:8477-8487. [PMID: 33817509 PMCID: PMC8015083 DOI: 10.1021/acsomega.1c00273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/09/2021] [Indexed: 05/04/2023]
Abstract
Opportunistic fungal infections caused by Cryptococcus neoformans are a significant source of mortality in immunocompromised patients. They are challenging to treat because of a limited number of antifungal drugs, and novel and more effective anticryptococcal therapies are needed. Ciclopirox olamine, a N-hydroxypyridone, has been in use as an approved therapeutic agent for the treatment of topical fungal infections for more than two decades. It is a fungicide, with broad activity across multiple fungal species. We synthesized 10 N-hydroxypyridone derivatives to develop an initial structure-activity understanding relative to efficacy as a starting point for the development of systemic antifungals. We screened the derivatives for antifungal activity against C. neoformans and Cryptococcus gattii and counter-screened for specificity in Candida albicans and two Malassezia species. Eight of the ten show inhibition at 1-3 μM concentration (0.17-0.42 μg per mL) in both Cryptococcus species and in C. albicans, but poor activity in the Malassezia species. In C. neoformans, the N-hydroxypyridones are fungicides, are not antagonistic with either fluconazole or amphotericin B, and are synergistic with multiple inhibitors of the mitochondrial electron transport chain. They appear to function primarily by chelating iron within the active site of iron-dependent enzymes. This preliminary structure-activity relationship points to the need for a lipophilic functional group at position six of the N-hydroxypyridone ring and identifies positions four and six as sites where further substitution may be tolerated. These molecules provide a clear starting point for future optimization for efficacy and target identification.
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Affiliation(s)
- Jeffrey Lin
- Department
of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, Missouri 63103, United States
| | - Maryam Zangi
- Department
of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
| | | | - Makala Shakar Reddy
- Medicinal
Chemistry Division, Albany Molecular Research
Inc., MN Park, Turkpally
Shamirpet Mandal, Genome Valley, Hyderabad 500078, India
| | - Lingala Vijaya Raghava Reddy
- Medicinal
Chemistry Division, Albany Molecular Research
Inc., MN Park, Turkpally
Shamirpet Mandal, Genome Valley, Hyderabad 500078, India
| | - Subir Kumar Sadhukhan
- Medicinal
Chemistry Division, Albany Molecular Research
Inc., MN Park, Turkpally
Shamirpet Mandal, Genome Valley, Hyderabad 500078, India
| | - Daniel P. Bradley
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Brenda Moreira-Walsh
- Edward
A. Doisy Department of Biochemistry, Saint
Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United
States
| | - Tiffany C. Edwards
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - Austin T. O’Dea
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
| | - John E. Tavis
- Department
of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Marvin J. Meyers
- Department
of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri 63103, United States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
| | - Maureen J. Donlin
- Edward
A. Doisy Department of Biochemistry, Saint
Louis University School of Medicine, 1100 South Grand Blvd., St. Louis, Missouri 63104, United
States
- Institute
for Drug and Biotherapeutic Innovation, Saint Louis University, St. Louis, Missouri 63103, United States
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13
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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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14
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Dandri M, Petersen J. cccDNA Maintenance in Chronic Hepatitis B - Targeting the Matrix of Viral Replication. Infect Drug Resist 2020; 13:3873-3886. [PMID: 33149632 PMCID: PMC7605611 DOI: 10.2147/idr.s240472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/02/2020] [Indexed: 12/11/2022] Open
Abstract
Chronic hepatitis B is a numerically important cause of cirrhosis and hepatocellular carcinoma, despite an effective prophylactic vaccine and well-tolerated and effective oral antivirals. Both the incapacity of the immune system to clear hepatitis B virus (HBV) infection and the unique replication strategies adopted by HBV are considered key determinants of HBV chronicity. In this regard, the formation of the HBV DNA minichromosome, the covalently closed circular DNA (cccDNA), in the nucleus of infected hepatocytes, is essential not only for the production of all viral proteins but also for HBV persistence even after long-term antiviral therapy. Licensed polymerase inhibitors target the HBV reverse transcriptase activity, control the disease with long-term therapy but fail to eliminate the cccDNA. Consequently, the production of viral RNAs and proteins, including the hepatitis B surface antigen (HBsAg), is not abolished. Novel therapeutic efforts that are in the pipeline for early clinical trials explore novel targets and molecules. Such therapeutic efforts focus on achieving a functional cure, which is defined by the loss of HBsAg and undetectable HBV DNA levels in serum. Since a true cure of HBV infection requires the elimination of the cccDNA from infected cells, comprehension of the mechanisms implicated in cccDNA biogenesis, regulation and stability appears necessary to achieve HBV eradication. In this review, we will summarize the state of knowledge on cccDNA metabolism, focusing on insights suggesting potential weak points of the cccDNA that may be key for the development of therapeutic approaches and design of clinical trials aiming at lowering cccDNA loads and activity.
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Affiliation(s)
- Maura Dandri
- Department of Internal Medicine, University Medical Center Hamburg - Eppendorf, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Luebeck-Borstel-Riems Site, Germany
| | - Joerg Petersen
- Institute for Interdisciplinary Medicine, Asklepios Klinik St Georg, University of Hamburg, Hamburg, Germany
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15
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Bak E, Miller JT, Noronha A, Tavis J, Gallicchio E, Murelli RP, Le Grice SFJ. 3,7-Dihydroxytropolones Inhibit Initiation of Hepatitis B Virus Minus-Strand DNA Synthesis. Molecules 2020; 25:molecules25194434. [PMID: 32992516 PMCID: PMC7583054 DOI: 10.3390/molecules25194434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 02/07/2023] Open
Abstract
Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral reverse transcriptase with epsilon (ε), a cis-acting regulatory signal located at the 5' terminus of pre-genomic RNA (pgRNA), and several host-encoded chaperone proteins. Binding of the viral polymerase (P protein) to ε is necessary for pgRNA encapsidation and synthesis of a short primer covalently attached to its terminal domain. Although we identified small molecules that recognize HBV ε RNA, these failed to inhibit protein-primed DNA synthesis. However, since initiation of HBV (-) strand DNA synthesis occurs within a complex of viral and host components (e.g., Hsp90, DDX3 and APOBEC3G), we considered an alternative therapeutic strategy of allosteric inhibition by disrupting the initiation complex or modifying its topology. To this end, we show here that 3,7-dihydroxytropolones (3,7-dHTs) can inhibit HBV protein-primed DNA synthesis. Since DNA polymerase activity of a ribonuclease (RNase H)-deficient HBV reverse transcriptase that otherwise retains DNA polymerase function is also abrogated, this eliminates direct involvement of RNase (ribonuclease) H activity of HBV reverse transcriptase and supports the notion that the HBV initiation complex might be therapeutically targeted. Modeling studies also provide a rationale for preferential activity of 3,7-dHTs over structurally related α-hydroxytropolones (α-HTs).
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Affiliation(s)
- Ellen Bak
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
| | - Jennifer T. Miller
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
| | - Andrea Noronha
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
| | - John Tavis
- Department of Molecular Microbiology and Immunology, St. Louis University, St. Louis, MO 63104, USA;
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY 11210, USA; (E.G.); (R.P.M.)
- PhD Program in Chemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
| | - Ryan P. Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY 11210, USA; (E.G.); (R.P.M.)
- PhD Program in Chemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
| | - Stuart F. J. Le Grice
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
- Correspondence:
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16
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Martinez MG, Villeret F, Testoni B, Zoulim F. Can we cure hepatitis B virus with novel direct-acting antivirals? Liver Int 2020; 40 Suppl 1:27-34. [PMID: 32077597 DOI: 10.1111/liv.14364] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 12/27/2019] [Indexed: 12/12/2022]
Abstract
Current treatments against chronic hepatitis B (CHB) include pegylated interferon alpha (Peg-IFNα) and nucleos(t)ide analogs (NAs), the latter targeting the viral retrotranscriptase, thus inhibiting de novo viral production. Although these therapies control infection and improve the patient's quality of life, they do not cure HBV-infected hepatocytes. A complete HBV cure is currently not possible because of the presence of the stable DNA intermediate covalently closed circular DNA (cccDNA). Current efforts are focused on achieving a functional cure, defined by the loss of Hepatitis B surface antigen (HBsAg) and undetectable HBV DNA levels in serum, and on exploring novel targets and molecules that are in the pipeline for early clinical trials. The likelihood of achieving a long-lasting functional cure, with no rebound after therapy cessation, is higher using combination therapies targeting different steps in the hepatitis B virus (HBV) replication cycle. Novel treatments and their combinations are discussed for their potential to cure HBV infection, as well as exciting new technologies that could directly target cccDNA and cure without killing the infected cells.
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Affiliation(s)
- Maria G Martinez
- Cancer Research Center of Lyon (CRCL), Lyon, France.,INSERM, U1052, Lyon, France
| | - François Villeret
- Cancer Research Center of Lyon (CRCL), Lyon, France.,INSERM, U1052, Lyon, France
| | - Barbara Testoni
- Cancer Research Center of Lyon (CRCL), Lyon, France.,INSERM, U1052, Lyon, France
| | - Fabien Zoulim
- Cancer Research Center of Lyon (CRCL), Lyon, France.,INSERM, U1052, Lyon, France.,Hospices Civils de Lyon (HCL), Lyon, France.,University of Lyon, UMR_S1052, UCBL, Lyon, France.,Institut Universitaire de France (IUF), Paris, France
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17
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Agyemang NB, Kukla CR, Edwards TC, Li Q, Langen MK, Schaal A, Franson AD, Casals AG, Donald KA, Yu AJ, Donlin MJ, Morrison LA, Tavis JE, Murelli RP. Divergent synthesis of a thiolate-based α-hydroxytropolone library with a dynamic bioactivity profile. RSC Adv 2019; 9:34227-34234. [PMID: 33042521 PMCID: PMC7543996 DOI: 10.1039/c9ra06383h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Here we describe a rapid and divergent synthetic route toward structurally novel αHTs functionalized with either one or two thioether or sulfonyl appendages. Evaluation of this library against hepatitis B and herpes simplex virus, as well as the pathogenic fungus Cryptococcus neoformans, and a human hepatoblastoma (HepDES19) revealed complementary biological profiles and new lead compounds with sub-micromolar activity against each pathogen.
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Affiliation(s)
- Nana B Agyemang
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, New York 11210, United States.,PhD Program in Chemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States
| | - Cassandra R Kukla
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Tiffany C Edwards
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Qilan Li
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Madison K Langen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, 63104, United States
| | - Alexandra Schaal
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, 63104, United States
| | - Abaigeal D Franson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Andreu Gazquez Casals
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Katherine A Donald
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Alice J Yu
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Maureen J Donlin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, 63104, United States
| | - Lynda A Morrison
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States.,Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, Missouri, 63110, United States
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, United States
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, New York 11210, United States.,PhD Program in Chemistry, The Graduate Center of The City University of New York, New York, New York 10016, United States
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18
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Tramontano E, Corona A, Menéndez-Arias L. Ribonuclease H, an unexploited target for antiviral intervention against HIV and hepatitis B virus. Antiviral Res 2019; 171:104613. [PMID: 31550450 DOI: 10.1016/j.antiviral.2019.104613] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/18/2022]
Abstract
Ribonucleases H (RNases H) are endonucleolytic enzymes, evolutionarily related to retroviral integrases, DNA transposases, resolvases and numerous nucleases. RNases H cleave RNA in RNA/DNA hybrids and their activity plays an important role in the replication of prokaryotic and eukaryotic genomes, as well as in the replication of reverse-transcribing viruses. During reverse transcription, the RNase H activity of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) degrades the viral genomic RNA to facilitate the synthesis of viral double-stranded DNA. HIV and HBV reverse transcriptases contain DNA polymerase and RNase H domains that act in a coordinated manner to produce double-stranded viral DNA. Although RNase H inhibitors have not been developed into licensed drugs, recent progress has led to the identification of a number of small molecules with inhibitory activity at low micromolar or even nanomolar concentrations. These compounds can be classified into metal-chelating active site inhibitors and allosteric inhibitors. Among them, α-hydroxytropolones, N-hydroxyisoquinolinediones and N-hydroxypyridinediones represent chemotypes active against both HIV and HBV RNases H. In this review we summarize recent developments in the field including the identification of novel RNase H inhibitors, compounds with dual inhibitory activity, broad specificity and efforts to decrease their toxicity.
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Affiliation(s)
- Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
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19
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Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
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Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
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20
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Cao F, Orth C, Donlin MJ, Adegboyega P, Meyers MJ, Murelli RP, Elagawany M, Elgendy B, Tavis JE. Synthesis and Evaluation of Troponoids as a New Class of Antibiotics. ACS OMEGA 2018; 3:15125-15133. [PMID: 30533576 PMCID: PMC6275967 DOI: 10.1021/acsomega.8b01754] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/19/2018] [Indexed: 05/11/2023]
Abstract
Novel antibiotics are urgently needed. The troponoids [tropones, tropolones, and α-hydroxytropolones (α-HT)] can have anti-bacterial activity. We synthesized or purchased 92 troponoids and evaluated their antibacterial activities against Staphylococcus aureus, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. Preliminary hits were assessed for minimum inhibitory concentrations (MIC80) and cytotoxicity (CC50) against human hepatoma cells. Sixteen troponoids inhibited S. aureus/E. coli/A. baumannii growth by ≥80% growth at <30 μM with CC50 values >50 μM. Two selected tropolones (63 and 285) inhibited 18 methicillin-resistant S. aureus (MRSA) strains with similar MIC80 values as against a reference strain. Two selected thiotropolones (284 and 363) inhibited multidrug-resistant (MDR) E. coli with MIC80 ≤30 μM. One α-HT (261) inhibited MDR-A. baumannii with MIC80 ≤30 μM. This study opens new avenues for development of novel troponoid antibiotics to address the critical need to combat MDR bacterial infections.
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Affiliation(s)
- Feng Cao
- John
Cochran Division, Department of Veterans Affairs Medical Center, 915 North Grand Blvd., St. Louis, Missouri 63106, United States
- E-mail: . Phone: +1 (314) 289-6358. Fax: +1(314) 289-7920 (F.C.)
| | - Cari Orth
- John
Cochran Division, Department of Veterans Affairs Medical Center, 915 North Grand Blvd., St. Louis, Missouri 63106, United States
| | - Maureen J. Donlin
- Edward
A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Patrick Adegboyega
- John
Cochran Division, Department of Veterans Affairs Medical Center, 915 North Grand Blvd., St. Louis, Missouri 63106, United States
| | - Marvin J. Meyers
- Department
of Chemistry, Saint Louis University, St. Louis, Missouri 63104, United States
| | - Ryan P. Murelli
- Department
of Chemistry, Brooklyn College, The City
University of New York, Brooklyn, New York 11210, United States
- PhD
Program in Chemistry, The Graduate Center
of The City University of New York, New York 10016, United
States
| | - Mohamed Elagawany
- Center for
Clinical Pharmacology, Washington University
School of Medicine and St. Louis College of Pharmacy, St. Louis, Missouri 63110, United States
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Damanhour University, Damanhour 31111, Egypt
| | - Bahaa Elgendy
- Center for
Clinical Pharmacology, Washington University
School of Medicine and St. Louis College of Pharmacy, St. Louis, Missouri 63110, United States
- Chemistry
Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - John E. Tavis
- Department
of Molecular Microbiology and Immunology, The Saint Louis University Liver Center, Saint Louis University School
of Medicine, St. Louis, Missouri 63104, United
States
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Levrero M, Subic M, Villeret F, Zoulim F. Perspectives and limitations for nucleo(t)side analogs in future HBV therapies. Curr Opin Virol 2018; 30:80-89. [DOI: 10.1016/j.coviro.2018.04.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/12/2022]
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