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Tatar E, Yaldız S, Kulabaş N, Vanderlinden E, Naesens L, Küçükgüzel İ. Synthesis and structure-activity relationship of L-methionine-coupled 1,3,4-thiadiazole derivatives with activity against influenza virus. Chem Biol Drug Des 2021; 99:398-415. [PMID: 34873848 DOI: 10.1111/cbdd.13995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 09/17/2021] [Accepted: 11/14/2021] [Indexed: 01/03/2023]
Abstract
In previous investigations, we identified a class of 1,3,4-thiadiazole derivatives with antiviral activity. N-{3-(Methylsulfanyl)-1-[5-(phenylamino)-1,3,4-thiadiazole-2-yl]propyl}benzamide emerged as a relevant lead compound for designing novel influenza A virus inhibitors. In the present study, we elaborated on this initial lead by performing chemical synthesis and antiviral evaluation of a series of structural analogues. During this research, thirteen novel 1,3,4-thiadiazole derivatives were synthesized by the cyclization of the corresponding thiosemicarbazides as synthetic precursors. The structures and the purities of the synthesized compounds were confirmed through chromatographic and spectral data. Four L-methionine-based 1,3,4-thiadiazole derivatives displayed activity against influenza A virus, the two best compounds being 24 carrying a 5-(4-chlorophenylamino)-1,3,4-thiadiazole moiety and 30 possessing a 5-(benzoylamino)-1,3,4-thiadiazole structure [antiviral EC50 against influenza A/H3N2 virus: 4.8 and 7.4 µM, respectively]. The 1,3,4-thiadiazole derivatives were inactive against influenza B virus and a wide panel of unrelated DNA and RNA viruses. Compound 24 represents a new class of selective influenza A virus inhibitors acting during the virus entry process, as evidenced by our findings in a time-of-addition assay. Molecular descriptors and in silico prediction of ADMET properties of the active compounds were calculated. According to in silico ADMET and drug similarity studies, active compounds have been estimated to be good candidates for oral administration with no apparent toxicity considerations.
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Affiliation(s)
- Esra Tatar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, İstanbul, Turkey
| | - Seda Yaldız
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, İstanbul, Turkey
| | - Necla Kulabaş
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, İstanbul, Turkey
| | - Evelien Vanderlinden
- Laboratory of Virology and Chemotherapy, KU Leuven Rega Institute, Leuven, Belgium
| | - Lieve Naesens
- Laboratory of Virology and Chemotherapy, KU Leuven Rega Institute, Leuven, Belgium
| | - İlkay Küçükgüzel
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, İstanbul, Turkey
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Popova EA, Kornev AA, Bessonov VV, Androsov DA, Petrov ML, Boitsov VM, Stepakov AV. In Vitro Activity of Organochalcogen Compounds: III. Cytotoxic Effect of 4-(2-Hydroxyaryl)-1,2,3-thiadiazoles Against K562 and Hela Tumor Cell Lines. RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363220120270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Remizov YO, Kornev AA, Pevzner LM, Petrov ML, Boitsov VM, Stepakov AV. In Vitro Activity of Organochalcogen Compounds: I. Cytotoxic Effect of 4-(1,2,3-Thiadiazol-4-yl)furans Against K562 and HeLa Tumor Cell Lines. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220110328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ferla S, Manganaro R, Benato S, Paulissen J, Neyts J, Jochmans D, Brancale A, Bassetto M. Rational modifications, synthesis and biological evaluation of new potential antivirals for RSV designed to target the M2-1 protein. Bioorg Med Chem 2020; 28:115401. [PMID: 32143992 DOI: 10.1016/j.bmc.2020.115401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/21/2020] [Indexed: 11/27/2022]
Abstract
Respiratory syncytial virus (RSV) is the main cause of lower respiratory tract diseases in infants and young children, with potentially serious and fatal consequences associated with severe infections. Despite extensive research efforts invested in the identification of therapeutic measures, no vaccine is currently available, while treatment options are limited to ribavirin and palivizumab, which both present significant limitations. While clinical and pre-clinical candidates mainly target the viral fusion protein, the nucleocapsid protein or the viral polymerase, our focus has been the identification of new antiviral compounds targeting the viral M2-1 protein, thanks to the presence of a zinc-ejecting group in their chemical structure. Starting from an anti-RSV hit we had previously identified with an in silico structure-based approach, we have designed, synthesised and evaluated a new series of dithiocarbamate analogues, with which we have explored the antiviral activity of this scaffold. The findings presented in this work may provide the basis for the identification of a new antiviral lead to treat RSV infections.
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Affiliation(s)
- Salvatore Ferla
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff CF103NB, UK.
| | - Roberto Manganaro
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff CF103NB, UK
| | - Sara Benato
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff CF103NB, UK
| | - Jasmine Paulissen
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Johan Neyts
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Andrea Brancale
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff CF103NB, UK
| | - Marcella Bassetto
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff CF103NB, UK; Department of Chemistry, Swansea University, Swansea, UK
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Dick A, Cocklin S. Recent Advances in HIV-1 Gag Inhibitor Design and Development. Molecules 2020; 25:molecules25071687. [PMID: 32272714 PMCID: PMC7181048 DOI: 10.3390/molecules25071687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023] Open
Abstract
Acquired Immune Deficiency Syndrome (AIDS) treatment with combination antiretroviral therapy (cART) has improved the life quality of many patients since its implementation. However, resistance mutations and the accumulation of severe side effects associated with cART remain enormous challenges that need to be addressed with the continual design and redesign of anti-HIV drugs. In this review, we focus on the importance of the HIV-1 Gag polyprotein as the master coordinator of HIV-1 assembly and maturation and as an emerging drug target. Due to its multiple roles in the HIV-1 life cycle, the individual Gag domains are attractive but also challenging targets for inhibitor design. However, recent encouraging developments in targeting the Gag domains such as the capsid protein with highly potent and potentially long-acting inhibitors, as well as the exploration and successful targeting of challenging HIV-1 proteins such as the matrix protein, have demonstrated the therapeutic viability of this important protein. Such Gag-directed inhibitors have great potential for combating the AIDS pandemic and to be useful tools to dissect HIV-1 biology.
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Cascade reactions as efficient and universal tools for construction and modification of 6-, 5-, 4- and 3-membered sulfur heterocycles of biological relevance. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Iraci N, Tabarrini O, Santi C, Sancineto L. NCp7: targeting a multitask protein for next-generation anti-HIV drug development part 2. Noncovalent inhibitors and nucleic acid binders. Drug Discov Today 2018; 23:687-695. [PMID: 29326078 DOI: 10.1016/j.drudis.2018.01.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/25/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Abstract
Nucleocapsid protein 7 (NCp7) represents a viable target not yet reached by the currently available antiretrovirals. It is a small and highly basic protein, which is essential for multiple stages of the viral replicative cycle, with its structure preserved in all viral strains, including clinical isolates. NCp7 can be inhibited covalently, noncovalently and by shielding the nucleic acid (NA) substrates of its chaperone activity. Although covalent NCp7 inhibitors have already been detailed in the first part of this review series, the focus here is based on noncovalent and NA-binder inhibitors and on the analysis of the NCp7 3D structure to deliver fruitful insights for future drug design strategies.
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Affiliation(s)
- Nunzio Iraci
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Claudio Santi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Luca Sancineto
- Department of Heterorganic Chemistry, Centre of Molecular and Macromulecular Studies, Lodz, Poland.
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Duchowicz PR, Bacelo DE, Fioressi SE, Palermo V, Ibezim NE, Romanelli GP. QSAR studies of indoyl aryl sulfides and sulfones as reverse transcriptase inhibitors. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2069-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Asquith CRM, Konstantinova LS, Laitinen T, Meli ML, Poso A, Rakitin OA, Hofmann-Lehmann R, Hilton ST. Evaluation of Substituted 1,2,3-Dithiazoles as Inhibitors of the Feline Immunodeficiency Virus (FIV) Nucleocapsid Protein via a Proposed Zinc Ejection Mechanism. ChemMedChem 2016; 11:2119-2126. [DOI: 10.1002/cmdc.201600260] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/21/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher R. M. Asquith
- School of Pharmacy; Faculty of Life Sciences; University College London; London WC1N 1AX UK
- Clinical Laboratory & Center for Clinical Studies; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
| | - Lidia S. Konstantinova
- Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Moscow 119991 Russian Federation
- Nanotechnology Education and Research Center; South Ural State, University; Lenina Ave. 76 Chelyabinsk 454080 Russian Federation
| | - Tuomo Laitinen
- School of Pharmacy; Faculty of Health Sciences; University of Eastern, Finland; Kuopio 70211 Finland
| | - Marina L. Meli
- Clinical Laboratory & Center for Clinical Studies; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
| | - Antti Poso
- School of Pharmacy; Faculty of Health Sciences; University of Eastern, Finland; Kuopio 70211 Finland
| | - Oleg A. Rakitin
- Zelinsky Institute of Organic Chemistry; Russian Academy of Sciences; Moscow 119991 Russian Federation
- Nanotechnology Education and Research Center; South Ural State, University; Lenina Ave. 76 Chelyabinsk 454080 Russian Federation
| | - Regina Hofmann-Lehmann
- Clinical Laboratory & Center for Clinical Studies; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
| | - Stephen T. Hilton
- School of Pharmacy; Faculty of Life Sciences; University College London; London WC1N 1AX UK
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The new facile and straightforward method for the synthesis of 4 H -1,2,3-thiadiazolo[5,4- b ]indoles and determination of their antiproliferative activity. Eur J Med Chem 2016; 108:245-257. [DOI: 10.1016/j.ejmech.2015.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/05/2015] [Accepted: 11/05/2015] [Indexed: 01/05/2023]
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Kim MJ, Kim SH, Park JA, Yu KL, Jang SI, Kim BS, Lee ES, You JC. Identification and characterization of a new type of inhibitor against the human immunodeficiency virus type-1 nucleocapsid protein. Retrovirology 2015; 12:90. [PMID: 26545586 PMCID: PMC4636002 DOI: 10.1186/s12977-015-0218-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/22/2015] [Indexed: 01/18/2023] Open
Abstract
Background The human immunodeficiency virus type-1 (HIV-1) nucleocapsid protein (NC) is an essential and multifunctional protein involved in multiple stages of the viral life cycle such as reverse transcription, integration of proviral DNA, and especially genome RNA packaging. For this reason, it has been considered as an attractive target for the development of new anti-HIV drugs. Although a number of inhibitors of NC have been reported thus far, the search for NC-specific and functional inhibitor(s) with a good antiviral activity continues. Results In this study, we report the identification of A1752, a small molecule with inhibitory action against HIV-1 NC, which shows a strong antiviral efficacy and an IC50 around 1 μM. A1752 binds directly to HIV-1 NC, thereby inhibiting specific chaperone functions of NC including Psi RNA dimerization and complementary trans-activation response element (cTAR) DNA destabilization, and it also disrupts the proper Gag processing. Further analysis of the mechanisms of action of A1752 also showed that it generates noninfectious viral particles with defects in uncoating and reverse transcription in the infected cells. Conclusions These results demonstrate that A1752 is a specific and functional inhibitor of NC with a novel mode of action and good antiviral efficacy. Thus, this agent provides a new type of anti-HIV NC inhibitor candidate for further drug development. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0218-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Seon Hee Kim
- Avixgen Inc., Seoul, 137-701, Korea. .,National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | | | - Kyung Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | - Soo In Jang
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | | | - Eun Soo Lee
- National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
| | - Ji Chang You
- Avixgen Inc., Seoul, 137-701, Korea. .,National Research Laboratory of Molecular Virology, Department of Pathology, School of Medicine, The Catholic University of Korea, Seoul, 137-701, Korea.
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12
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Okazaki S, Oishi S, Mizuhara T, Shimura K, Murayama H, Ohno H, Matsuoka M, Fujii N. Investigations of possible prodrug structures for 2-(2-mercaptophenyl)tetrahydropyrimidines: reductive conversion from anti-HIV agents with pyrimidobenzothiazine and isothiazolopyrimidine scaffolds. Org Biomol Chem 2015; 13:4706-13. [PMID: 25800792 DOI: 10.1039/c5ob00301f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
3,4-Dihydro-2H,6H-pyrimido[1,2-c][1,3]benzothiazin-6-imine (PD 404182) and 3,4-dihydro-2H-benzo[4,5]isothiazolo[2,3-a]pyrimidine are the heterocyclic antiretroviral agents against human immunodeficiency virus type 1 (HIV-1) infection. On the basis of similar structure-activity relationships of anti-HIV activities toward the early-stage of viral infection between these unique scaffolds, the transformations under the bioassay conditions were investigated. The distinctive S-N bond in the isothiazolopyrimidine scaffold was immediately cleaved under reductive conditions in the presence of GSH to generate a thiophenol derivative. A similar rapid conversion of PD 404182 into the same thiophenol derivative was observed, suggesting that pyrimidobenzothiazine and isothiazolopyrimidine scaffolds may work as prodrug forms of the common bioactive thiophenol derivatives.
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Affiliation(s)
- Shiho Okazaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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Mori M, Kovalenko L, Lyonnais S, Antaki D, Torbett BE, Botta M, Mirambeau G, Mély Y. Nucleocapsid Protein: A Desirable Target for Future Therapies Against HIV-1. Curr Top Microbiol Immunol 2015; 389:53-92. [PMID: 25749978 PMCID: PMC7122173 DOI: 10.1007/82_2015_433] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The currently available anti-HIV-1 therapeutics is highly beneficial to infected patients. However, clinical failures occur as a result of the ability of HIV-1 to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by available therapies. In this respect, the nucleocapsid (NC) protein, a zinc finger protein, is particularly attractive, as it is highly conserved and plays a central role in virus replication, mainly by interacting with nucleic acids. The compelling rationale for considering NC as a viable drug target is illustrated by the fact that point mutants of this protein lead to noninfectious viruses and by the inability to select viruses resistant to a first generation of anti-NC drugs. In our review, we discuss the most relevant properties and functions of NC, as well as recent developments of small molecules targeting NC. Zinc ejectors show strong antiviral activity, but are endowed with a low therapeutic index due to their lack of specificity, which has resulted in toxicity. Currently, they are mainly being investigated for use as topical microbicides. Greater specificity may be achieved by using non-covalent NC inhibitors (NCIs) targeting the hydrophobic platform at the top of the zinc fingers or key nucleic acid partners of NC. Within the last few years, innovative methodologies have been developed to identify NCIs. Though the antiviral activity of the identified NCIs needs still to be improved, these compounds strongly support the druggability of NC and pave the way for future structure-based design and optimization of efficient NCIs.
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Affiliation(s)
- Mattia Mori
- Dipartimento di Biotecnologie Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
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14
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Rozin Y, Zhidovinov S, Beryozkina T, Shafran Y, Lubec G, Eltsov O, Slepukhin P, Knippschild U, Bischof J, Dehaen W, Bakulev V. A novel transformation of β-1,2,3-thiadiazol-5-yl enamines into thieno[2,3-d]pyridazines. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Asquith CRM, Meli ML, Konstantinova LS, Laitinen T, Poso A, Rakitin OA, Hofmann-Lehmann R, Allenspach K, Hilton ST. Novel fused tetrathiocines as antivirals that target the nucleocapsid zinc finger containing protein of the feline immunodeficiency virus (FIV) as a model of HIV infection. Bioorg Med Chem Lett 2014; 25:1352-5. [PMID: 25702849 DOI: 10.1016/j.bmcl.2014.12.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 01/06/2023]
Abstract
A novel series of fused tetrathiocines were prepared for evaluation of activity against the nucleocapsid protein of the feline immunodeficiency virus (FIV) in an in vitro cell culture approach. The results demonstrated that the compounds display potent nanomolar activity and low toxicity against this key model of HIV infection.
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Affiliation(s)
- Christopher R M Asquith
- UCL School of Pharmacy, Faculty of Life Sciences, University College London, London WC1N 1AX, United Kingdom
| | - Marina L Meli
- Clinical Laboratory and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Lidia S Konstantinova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Oleg A Rakitin
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Regina Hofmann-Lehmann
- Clinical Laboratory and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Karin Allenspach
- Veterinary Clinical Sciences, Royal Veterinary College, Hatfield AL9 7TA, United Kingdom
| | - Stephen T Hilton
- UCL School of Pharmacy, Faculty of Life Sciences, University College London, London WC1N 1AX, United Kingdom.
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Garg D, Torbett BE. Advances in targeting nucleocapsid-nucleic acid interactions in HIV-1 therapy. Virus Res 2014; 193:135-43. [PMID: 25026536 PMCID: PMC4252855 DOI: 10.1016/j.virusres.2014.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.
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Affiliation(s)
- Divita Garg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Dianova LN, Berseneva VS, El’tsov OS, Fan ZJ, Bakulev VA. Reactions of Malonothioamide Derivatives with Azides*. Chem Heterocycl Compd (N Y) 2014. [DOI: 10.1007/s10593-014-1552-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Mitra M, Wang W, Vo MN, Rouzina I, Barany G, Musier-Forsyth K. The N-terminal zinc finger and flanking basic domains represent the minimal region of the human immunodeficiency virus type-1 nucleocapsid protein for targeting chaperone function. Biochemistry 2013; 52:8226-36. [PMID: 24144434 DOI: 10.1021/bi401250a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein is a chaperone that facilitates nucleic acid conformational changes to produce the most thermodynamically stable arrangement. The critical role of NC in many steps of the viral life cycle makes it an attractive therapeutic target. The chaperone activity of NC depends on its nucleic acid aggregating ability, duplex destabilizing activity, and rapid on-off binding kinetics. During the minus-strand transfer step of reverse transcription, NC chaperones the annealing of highly structured transactivation response region (TAR) RNA to the complementary TAR DNA. In this work, the role of different functional domains of NC in facilitating 59-nucleotide TAR RNA-DNA annealing was probed by using chemically synthesized peptides derived from full-length (55 amino acids) HIV-1 NC: NC(1-14), NC(15-35), NC(1-28), NC(1-35), NC(29-55), NC(36-55), and NC(11-55). Most of these peptides displayed significantly reduced annealing kinetics, even when present at concentrations much higher than that of wild-type (WT) NC. In addition, these truncated NC constructs generally bind more weakly to single-stranded DNA and are less effective nucleic acid aggregating agents than full-length NC, consistent with the loss of both electrostatic and hydrophobic contacts. However, NC(1-35) displayed annealing kinetics, nucleic acid binding, and aggregation activity that were very similar to those of WT NC. Thus, we conclude that the N-terminal zinc finger, flanked by the N-terminus and linker domains, represents the minimal sequence that is necessary and sufficient for chaperone function in vitro. In addition, covalent continuity of the 35 N-terminal amino acids of NC is critical for full activity. Thus, although the hydrophobic pocket formed by residues proximal to the C-terminal zinc finger has been a major focus of recent anti-NC therapeutic strategies, NC(1-35) represents an alternative target for therapeutics aimed at disrupting NC's chaperone function.
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Affiliation(s)
- Mithun Mitra
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University , Columbus, Ohio 43210, United States
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Hergott CB, Mitra M, Guo J, Wu T, Miller JT, Iwatani Y, Gorelick RJ, Levin JG. Zinc finger function of HIV-1 nucleocapsid protein is required for removal of 5'-terminal genomic RNA fragments: a paradigm for RNA removal reactions in HIV-1 reverse transcription. Virus Res 2013; 171:346-55. [PMID: 23149014 PMCID: PMC3578084 DOI: 10.1016/j.virusres.2012.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/27/2012] [Accepted: 08/20/2012] [Indexed: 11/28/2022]
Abstract
During (-) strong-stop DNA [(-) SSDNA] synthesis, RNase H cleavage of genomic viral RNA generates small 5'-terminal RNA fragments (14-18 nt) that remain annealed to the DNA. Unless these fragments are removed, the minus-strand transfer reaction, required for (-) SSDNA elongation, cannot occur. Here, we describe the mechanism of 5'-terminal RNA removal and the roles of HIV-1 nucleocapsid protein (NC) and RNase H cleavage in this process. Using an NC-dependent system that models minus-strand transfer, we show that the presence of short terminal fragments pre-annealed to (-) SSDNA has no impact on strand transfer, implying efficient fragment removal. Moreover, in reactions with an RNase H(-) reverse transcriptase mutant, NC alone is able to facilitate fragment removal, albeit less efficiently than in the presence of both RNase H activity and NC. Results obtained from novel electrophoretic gel mobility shift and Förster Resonance Energy Transfer assays, which each directly measure RNA fragment release from a duplex in the absence of DNA synthesis, demonstrate for the first time that the architectural integrity of NC's zinc finger (ZF) domains is absolutely required for this reaction. This suggests that NC's helix destabilizing activity (associated with the ZFs) facilitates strand exchange through the displacement of these short terminal RNAs by the longer 3' acceptor RNA, which forms a more stable duplex with (-) SSDNA. Taken together with previously published results, we conclude that NC-mediated fragment removal is linked mechanistically with selection of the correct primer for plus-strand DNA synthesis and tRNA removal step prior to plus-strand transfer. Thus, HIV-1 has evolved a single mechanism for these RNA removal reactions that are critical for successful reverse transcription.
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MESH Headings
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Gene Expression Regulation, Viral
- HIV-1/chemistry
- HIV-1/genetics
- HIV-1/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Reverse Transcription
- Zinc Fingers
- gag Gene Products, Human Immunodeficiency Virus/chemistry
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Christopher B. Hergott
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
| | - Mithun Mitra
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
| | - Jianhui Guo
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
| | - Tiyun Wu
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
| | - Jennifer T. Miller
- Reverse Transcriptase Biochemistry Section, HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Yasumasa Iwatani
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Judith G. Levin
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
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20
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Vercruysse T, Basta B, Dehaen W, Humbert N, Balzarini J, Debaene F, Sanglier-Cianférani S, Pannecouque C, Mély Y, Daelemans D. A phenyl-thiadiazolylidene-amine derivative ejects zinc from retroviral nucleocapsid zinc fingers and inactivates HIV virions. Retrovirology 2012; 9:95. [PMID: 23146561 PMCID: PMC3542062 DOI: 10.1186/1742-4690-9-95] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/24/2012] [Indexed: 11/25/2022] Open
Abstract
Background Sexual acquisition of the human immunodeficiency virus (HIV) through mucosal transmission may be prevented by using topically applied agents that block HIV transmission from one individual to another. Therefore, virucidal agents that inactivate HIV virions may be used as a component in topical microbicides. Results Here, we have identified 2-methyl-3-phenyl-2H-[1,2,4]thiadiazol-5-ylideneamine (WDO-217) as a low-molecular-weight molecule that inactivates HIV particles. Both HIV-1 and HIV-2 virions pretreated with this compound were unable to infect permissive cells. Moreover, WDO-217 was able to inhibit infections of a wide spectrum of wild-type and drug-resistant HIV-1, including clinical isolates, HIV-2 and SIV strains. Whereas the capture of virus by DC-SIGN was unaffected by the compound, it efficiently prevented the transmission of DC-SIGN-captured virus to CD4+ T-lymphocytes. Interestingly, exposure of virions to WDO-217 reduced the amount of virion-associated genomic RNA as measured by real-time RT-qPCR. Further mechanism-of-action studies demonstrated that WDO-217 efficiently ejects zinc from the zinc fingers of the retroviral nucleocapsid protein NCp7 and inhibits the cTAR destabilization properties of this protein. Importantly, WDO-217 was able to eject zinc from both zinc fingers, even when NCp7 was bound to oligonucleotides, while no covalent interaction between NCp7 and WDO-217 could be observed. Conclusion This compound is a new lead structure that can be used for the development of a new series of NCp7 zinc ejectors as candidate topical microbicide agents.
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Affiliation(s)
- Thomas Vercruysse
- Rega Institute for Medical Research, Laboratory for Virology and Chemotherapy, KU Leuven, Minderbroedersstraat 10, Leuven, B-3000, Belgium
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21
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The Continuing Evolution of HIV-1 Therapy: Identification and Development of Novel Antiretroviral Agents Targeting Viral and Cellular Targets. Mol Biol Int 2012; 2012:401965. [PMID: 22848825 PMCID: PMC3400388 DOI: 10.1155/2012/401965] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/24/2012] [Accepted: 05/11/2012] [Indexed: 11/18/2022] Open
Abstract
During the past three decades, over thirty-five anti-HIV-1 therapies have been developed for use in humans and the progression from monotherapeutic treatment regimens to today's highly active combination antiretroviral therapies has had a dramatic impact on disease progression in HIV-1-infected individuals. In spite of the success of AIDS therapies and the existence of inhibitors of HIV-1 reverse transcriptase, protease, entry and fusion, and integrase, HIV-1 therapies still have a variety of problems which require continued development efforts to improve efficacy and reduce toxicity, while making drugs that can be used throughout both the developed and developing world, in pediatric populations, and in pregnant women. Highly active antiretroviral therapies (HAARTs) have significantly delayed the progression to AIDS, and in the developed world HIV-1-infected individuals might be expected to live normal life spans while on lifelong therapies. However, the difficult treatment regimens, the presence of class-specific drug toxicities, and the emergence of drug-resistant virus isolates highlight the fact that improvements in our therapeutic regimens and the identification of new and novel viral and cellular targets for therapy are still necessary. Antiretroviral therapeutic strategies and targets continue to be explored, and the development of increasingly potent molecules within existing classes of drugs and the development of novel strategies are ongoing.
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22
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Mori M, Schult-Dietrich P, Szafarowicz B, Humbert N, Debaene F, Sanglier-Cianferani S, Dietrich U, Mély Y, Botta M. Use of virtual screening for discovering antiretroviral compounds interacting with the HIV-1 nucleocapsid protein. Virus Res 2012; 169:377-87. [PMID: 22634301 DOI: 10.1016/j.virusres.2012.05.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 12/16/2022]
Abstract
The HIV-1 nucleocapsid protein (NC) is considered as an emerging drug target for the therapy of AIDS. Several studies have highlighted the crucial role of NC within the viral replication cycle. However, although NC inhibition has provided in vitro and in vivo antiretroviral activity, drug-candidates which interfere with NC functions are still missing in the therapeutic arsenal against HIV. Based on previous studies, where the dynamic behavior of NC and its ligand binding properties have been investigated by means of computational methods, here we used a virtual screening protocol for discovering novel antiretroviral compounds which interact with NC. The antiretroviral activity of virtual hits was tested in vitro, whereas biophysical studies elucidated the direct interaction of most active compounds with NC(11-55), a peptide corresponding to the zinc finger domain of NC. Two novel antiretroviral small molecules capable of interacting with NC are presented here.
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Affiliation(s)
- Mattia Mori
- Università di Roma La Sapienza, Dipartimento di Chimica e Tecnologie del Farmaco, piazzale A. Moro 5, I-00185 Roma, Italy
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23
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Parent LJ, Gudleski N. Beyond plasma membrane targeting: role of the MA domain of Gag in retroviral genome encapsidation. J Mol Biol 2011; 410:553-64. [PMID: 21762800 DOI: 10.1016/j.jmb.2011.04.072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/27/2011] [Accepted: 04/29/2011] [Indexed: 01/16/2023]
Abstract
The MA (matrix) domain of the retroviral Gag polyprotein plays several critical roles during virus assembly. Although best known for targeting the Gag polyprotein to the inner leaflet of the plasma membrane for virus budding, recent studies have revealed that MA also contributes to selective packaging of the genomic RNA (gRNA) into virions. In this Review, we summarize recent progress in understanding how MA participates in genome incorporation. We compare the mechanisms by which the MA domains of different retroviral Gag proteins influence gRNA packaging, highlighting variations and similarities in how MA directs the subcellular trafficking of Gag, interacts with host factors and binds to nucleic acids. A deeper understanding of how MA participates in these diverse functions at different stages in the virus assembly pathway will require more detailed information about the structure of the MA domain within the full-length Gag polyprotein. In particular, it will be necessary to understand the structural basis of the interaction of MA with gRNA, host transport factors and membrane phospholipids. A better appreciation of the multiple roles MA plays in genome packaging and Gag localization might guide the development of novel antiviral strategies in the future.
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Affiliation(s)
- Leslie J Parent
- Department of Medicine, Penn State College of Medicine, The Milton S. Hershey Medical Center, Hershey, PA 17033, USA.
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24
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An extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast Dicer. EMBO J 2011; 30:4223-35. [PMID: 21847092 PMCID: PMC3199388 DOI: 10.1038/emboj.2011.300] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 07/22/2011] [Indexed: 01/06/2023] Open
Abstract
The Dicer ribonuclease Dcr1 plays an important role in the biogenesis of small regulatory RNAs. Surprisingly, RNA binding by the double-stranded RNA binding domain (dsRBD) is dispensable for Dcr1 function, while zinc coordination of the extended dsRBD is required for its nuclear localization and RNA silencing. Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here, we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel zinc-binding motif that is conserved among dicers in yeast. Although the C-terminal domain of Dcr1 still binds nucleic acids, this property is dispensable for proper functioning of Dcr1. In contrast, disruption of zinc coordination renders Dcr1 mainly cytoplasmic and leads to remarkable changes in gene expression and loss of heterochromatin assembly. In summary, our results reveal novel insights into the mechanism of nuclear retention of Dcr1 and raise the possibility that this new class of dsRBDs might generally function in nucleocytoplasmic trafficking and not substrate binding. The C-terminal domain of Dcr1 constitutes a novel regulatory module that might represent a potential target for therapeutic intervention with fungal diseases.
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25
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Daelemans D, Pauwels R, De Clercq E, Pannecouque C. A time-of-drug addition approach to target identification of antiviral compounds. Nat Protoc 2011; 6:925-33. [PMID: 21637207 PMCID: PMC7086561 DOI: 10.1038/nprot.2011.330] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Insight into the mode of action of newly discovered antiviral agents is now almost a prerequisite for clinical development. This protocol describes a method that provides information on the target of inhibitors of the human immunodeficiency virus (HIV); it can also be adapted to other viruses. The results from this experiment are available within 2 d. This time-based approach determines how long the addition of a compound can be postponed before losing its antiviral activity in cell culture. The target of an antiviral compound can be identified by comparing its relative position in the time scale to that of reference drugs. Therefore, it is more precise than, for example, in the case of HIV, a determination of pre- or postintegrational mode of action, and combines in one routine different assays for studying mechanisms of action.
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Affiliation(s)
- Dirk Daelemans
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium.
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26
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Wang S, Wang H, Fan Z, Fu Y, Mi N, Zhang J, Zhang Z, Belskaya NP, Bakulev VA. Synthesis of 3,5-Dichloro-4-(1,1,2,2-tetrafluoroethoxy)phenyl Containing 1,2,3-Thiadiazole Derivatives via Ugi Reaction and Their Biological Activities. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201190080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Wang H, Yang Z, Fan Z, Wu Q, Zhang Y, Mi N, Wang S, Zhang Z, Song H, Liu F. Synthesis and insecticidal activity of N-tert-butyl-N,N'-diacylhydrazines containing 1,2,3-thiadiazoles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:628-634. [PMID: 21166420 DOI: 10.1021/jf104004q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
N-tert-Butyl-N,N'-diacylhydrazines are nonsteroidal ecdysone agonists used as environmental benign pest regulators. In this paper, two series of new N-tert-butyl-N,N'-diacylhydrazine derivatives containing 1,2,3-thiadiazole were designed and synthesized. All structures of the synthesized compounds were confirmed by proton nuclear magnetic resonance ((1)H NMR), infrared spectroscopy (IR), and high-resolution mass spectrometry (HRMS). Bioasssay results indicated that most of the synthesized compounds possessed good insecticidal activities against Plutella xylostella L. and Culex pipiens pallens as compared with the positive control, tebufenozide. The results of this study indicated that 1,2,3-thiadiazoles, as an important active substructure, could improve or maintain the activity of the dicylhydrazines and favor novel pesticide development.
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Affiliation(s)
- Huan Wang
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, People's Republic of China
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28
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Quintal SM, dePaula QA, Farrell NP. Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences. Metallomics 2011; 3:121-39. [PMID: 21253649 DOI: 10.1039/c0mt00070a] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Zinc finger reactions with inorganic ions and coordination compounds are as diverse as the zinc fingers themselves. Use of metal ions such as Co(2+) and Cd(2+) has given structural, thermodynamic and kinetic information on zinc fingers and zinc-finger-DNA/RNA interactions. It is a general truism that alteration of the coordination sphere in the finger environment will disrupt the recognition with DNA/RNA and this has implications for mechanism of toxicity and carcinogenesis of metal ions. Structural zinc fingers are susceptible to electrophilic attack and the recognition that the coordination sphere of inorganic compounds may be modulated for control of electrophilic attack on zinc fingers raises the possibility of systematic studies of zinc fingers as drug targets using inorganic chemistry. Some inorganic compounds such as those of As(III) and Au(I) may exert their biological effects through inactivation of zinc fingers and novel approaches to specifically attack the zinc-bound ligands using Co(III)-Schiff bases and Platinum(II)-Nucleobase compounds have been proposed. The genomic importance of zinc fingers suggests that the "coordination chemistry" of zinc fingers themselves is ripe for exploration to design new targets for medicinal inorganic chemistry.
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Affiliation(s)
- Susana M Quintal
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main St., Richmond, VA 23284-2006, USA
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