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Cushing VI, Koh AF, Feng J, Jurgaityte K, Bondke A, Kroll SHB, Barbazanges M, Scheiper B, Bahl AK, Barrett AGM, Ali S, Kotecha A, Greber BJ. High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design. Nat Commun 2024; 15:2265. [PMID: 38480681 PMCID: PMC10937634 DOI: 10.1038/s41467-024-46375-9] [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: 07/04/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.
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Affiliation(s)
- Victoria I Cushing
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Adrian F Koh
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands
| | - Junjie Feng
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Kaste Jurgaityte
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | | | | | - Marion Barbazanges
- Department of Chemistry, Imperial College London, London, UK
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Bodo Scheiper
- Department of Chemistry, Imperial College London, London, UK
| | - Ash K Bahl
- Carrick Therapeutics, Nova UCD, Bellfield Innovation Park, Dublin 4, Ireland
| | | | - Simak Ali
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands.
| | - Basil J Greber
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
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2
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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3
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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [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: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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4
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Yu D, Wagner S, Schütz M, Jeon Y, Seo M, Kim J, Brückner N, Kicuntod J, Tillmanns J, Wangen C, Hahn F, Kaufer BB, Neipel F, Eickhoff J, Klebl B, Nam K, Marschall M. An Antiherpesviral Host-Directed Strategy Based on CDK7 Covalently Binding Drugs: Target-Selective, Picomolar-Dose, Cross-Virus Reactivity. Pharmaceutics 2024; 16:158. [PMID: 38399219 PMCID: PMC10892818 DOI: 10.3390/pharmaceutics16020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
The repertoire of currently available antiviral drugs spans therapeutic applications against a number of important human pathogens distributed worldwide. These include cases of the pandemic severe acute respiratory coronavirus type 2 (SARS-CoV-2 or COVID-19), human immunodeficiency virus type 1 (HIV-1 or AIDS), and the pregnancy- and posttransplant-relevant human cytomegalovirus (HCMV). In almost all cases, approved therapies are based on direct-acting antivirals (DAAs), but their benefit, particularly in long-term applications, is often limited by the induction of viral drug resistance or side effects. These issues might be addressed by the additional use of host-directed antivirals (HDAs). As a strong input from long-term experiences with cancer therapies, host protein kinases may serve as HDA targets of mechanistically new antiviral drugs. The study demonstrates such a novel antiviral strategy by targeting the major virus-supportive host kinase CDK7. Importantly, this strategy focuses on highly selective, 3D structure-derived CDK7 inhibitors carrying a warhead moiety that mediates covalent target binding. In summary, the main experimental findings of this study are as follows: (1) the in vitro verification of CDK7 inhibition and selectivity that confirms the warhead covalent-binding principle (by CDK-specific kinase assays), (2) the highly pronounced antiviral efficacies of the hit compounds (in cultured cell-based infection models) with half-maximal effective concentrations that reach down to picomolar levels, (3) a particularly strong potency of compounds against strains and reporter-expressing recombinants of HCMV (using infection assays in primary human fibroblasts), (4) additional activity against further herpesviruses such as animal CMVs and VZV, (5) unique mechanistic properties that include an immediate block of HCMV replication directed early (determined by Western blot detection of viral marker proteins), (6) a substantial drug synergism in combination with MBV (measured by a Loewe additivity fixed-dose assay), and (7) a strong sensitivity of clinically relevant HCMV mutants carrying MBV or ganciclovir resistance markers. Combined, the data highlight the huge developmental potential of this host-directed antiviral targeting concept utilizing covalently binding CDK7 inhibitors.
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Affiliation(s)
- DongHoon Yu
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Martin Schütz
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Yeejin Jeon
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Mooyoung Seo
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Jaeseung Kim
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Nadine Brückner
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Julia Tillmanns
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Christina Wangen
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Benedikt B. Kaufer
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7–13, 14163 Berlin, Germany
| | - Frank Neipel
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Jan Eickhoff
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
- The Norwegian College of Fishery Science UiT, Arctic University of Norway, 9037 Tromsø, Norway
| | - Kiyean Nam
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Manfred Marschall
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
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5
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Wild M, Karner D, Eickhoff J, Wagner S, Kicuntod J, Chang W, Barry P, Jonjić S, Lenac Roviš T, Marschall M. Combined Treatment with Host-Directed and Anticytomegaloviral Kinase Inhibitors: Mechanisms, Synergisms and Drug Resistance Barriers. Pharmaceutics 2023; 15:2680. [PMID: 38140021 PMCID: PMC10748244 DOI: 10.3390/pharmaceutics15122680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Despite the availability of currently approved antiviral drugs, infections with human cytomegalovirus (HCMV) still cause clinically challenging, sometimes life-threatening situations. There is an urgent need for enhanced anti-HCMV drugs that offer improved efficacy, reduced dosages and options for long-term treatment without risk of the development of viral drug resistance. Recently, we reported the pronounced anti-HCMV efficacy of pharmacological inhibitors of cyclin-dependent kinases (CDKs), in particular, the potential of utilizing drug synergies upon combination treatment with inhibitors of host CDKs and the viral CDK-like kinase pUL97 (vCDK/pUL97). Here, we expand this finding by further assessing the in vitro synergistic antiviral interaction between vCDK and CDK inhibitors towards HCMV as well as non-human cytomegaloviruses. An extension of this synergy approach was achieved in vivo by using the recombinant MCMV-UL97/mouse model, confirming the high potential of combination treatment with the clinically approved vCDK inhibitor maribavir (MBV) and the developmental CDK7 inhibitor LDC4297. Moreover, mechanistic aspects of this synergistic drug combination were illustrated on the levels of intracellular viral protein transport and viral genome replication. The analysis of viral drug resistance did not reveal resistance formation in the case of MBV + LDC4297 combination treatment. Spanning various investigational levels, these new results strongly support our concept, employing the great potential of anti-HCMV synergistic drug treatment.
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Affiliation(s)
- Markus Wild
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (S.W.); (J.K.)
| | - Dubravka Karner
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia; (D.K.); (S.J.); (T.L.R.)
| | - Jan Eickhoff
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany;
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (S.W.); (J.K.)
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (S.W.); (J.K.)
| | - William Chang
- Department of Medical Microbiology and Immunology, California National Primate Research Center, University of California, 3146 Tupper Hall, 1 Shields Avenue, Davis, CA 95616, USA; (W.C.); (P.B.)
| | - Peter Barry
- Department of Medical Microbiology and Immunology, California National Primate Research Center, University of California, 3146 Tupper Hall, 1 Shields Avenue, Davis, CA 95616, USA; (W.C.); (P.B.)
| | - Stipan Jonjić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia; (D.K.); (S.J.); (T.L.R.)
| | - Tihana Lenac Roviš
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Brace Branchetta 20, 51000 Rijeka, Croatia; (D.K.); (S.J.); (T.L.R.)
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (S.W.); (J.K.)
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6
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Schütz M, Wangen C, Sommerer M, Kögler M, Eickhoff J, Degenhart C, Klebl B, Naing Z, Egilmezer E, Hamilton ST, Rawlinson WD, Sticht H, Marschall M. Cytomegalovirus cyclin-dependent kinase ortholog vCDK/pUL97 undergoes regulatory interaction with human cyclin H and CDK7 to codetermine viral replication efficiency. Virus Res 2023; 335:199200. [PMID: 37591314 PMCID: PMC10445456 DOI: 10.1016/j.virusres.2023.199200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Human cytomegalovirus (HCMV) infection is shaped by a tightly regulated interplay between viral and cellular proteins. Distinct kinase activities, such as the viral cyclin-dependent kinase ortholog (vCDK) pUL97 and cellular CDK7 are both crucial for efficient viral replication. Previously, we reported that both kinases, vCDK/pUL97 and CDK7, interact with cyclin H, thereby achieving an enhanced level of kinase activity and overall functionality in viral replication. Here we provide a variety of novel results, as generated on a methodologically extended basis, and present a concept for the codetermination of viral replication efficiency through these kinase activities: (i) cyclin H expression, in various human cell types, is substantially upregulated by strains of HCMV including the clinically relevant HCMV Merlin; (ii) vCDK/pUL97 interacts with human cyclin H in both HCMV-infected and plasmid-transfected cell systems; (iii) a doxycycline-inducible shRNA-dependent knock-down (KD) of cyclin H significantly reduces pUL97 activity (qSox in vitro kinase assay); (iv) accordingly, pUL97 in vitro kinase activity is seen significantly increased upon addition of recombinant cyclin H; (v) as a point of specific importance, human CDK7 activity shows an increase by vCDK/pUL97-mediated trans-stimulation (whereas pUL97 is not stimulated by CDK7); (vi) phosphosite-specific antibodies indicate an upregulated CDK7 phosphorylation upon HCMV infection, as mediated through a pUL97-specific modulatory effect (i.e. shown by pUL97 inhibitor treatment or pUL97-deficient viral mutant); (vii) finally, an efficient KD of cyclin H in primary fibroblasts generally results in an impaired HCMV replication efficiency as measured on protein and genomic levels. These results show evidence for the codetermination of viral replication by vCDK/pUL97, cyclin H and CDK7, thus supporting the specific importance of cyclin H as a central regulatory factor, and suggesting novel targeting options for antiviral drugs.
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Affiliation(s)
- Martin Schütz
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany.
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany
| | - Mona Sommerer
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany
| | - Melanie Kögler
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany
| | | | | | - Bert Klebl
- Lead Discovery Center GmbH, Dortmund, Germany
| | - Zin Naing
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - Ece Egilmezer
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - Stuart T Hamilton
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - William D Rawlinson
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, FAU, Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany.
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7
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Syrigos GV, Feige M, Dirlam A, Businger R, Gruska I, Wiebusch L, Hamprecht K, Schindler M. Abemaciclib restricts HCMV replication by suppressing pUL97-mediated phosphorylation of SAMHD1. Antiviral Res 2023; 217:105689. [PMID: 37516154 DOI: 10.1016/j.antiviral.2023.105689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Human cytomegalovirus (HCMV) is a herpesvirus that causes life-threatening infections in newborns or immunosuppressed patients. For viral replication, HCMV establishes a network of cellular interactions, among others cyclin-dependent kinases (CDK). Furthermore, HCMV encodes pUL97, a viral kinase, which is a CDK-homologue. HCMV uses pUL97 in order to phosphorylate and thereby antagonize SAMHD1, an antiviral host cell factor. Since HCMV has several mechanisms to evade restriction by SAMHD1, we first analyzed the kinetics of SAMHD1-inactivation and found that phosphorylation of SAMHD1 by pUL97 occurs directly after infection of macrophages. We hence hypothesized that inhibition of this process qualifies as efficient antiviral target and FDA approved CDK-inhibitors (CDKIs) might be potent antivirals that prevent the inactivation of SAMHD1. Indeed, Abemaciclib, a 2nd generation CDKI exhibited superior IC50s against HCMV in infected macrophages and the antiviral activity largely relied on its ability to block pUL97-mediated SAMHD1-phosphorylation. Altogether, our study highlights the therapeutic potential of clinically-approved CDKIs as antivirals against HCMV, sheds light on their mode of action and establishes SAMHD1 as a valid and highly potent therapeutic target.
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Affiliation(s)
- Georgios Vavouras Syrigos
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Maximilian Feige
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Alicia Dirlam
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Ramona Businger
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Iris Gruska
- Laboratory of Molecular Pediatrics, Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lüder Wiebusch
- Laboratory of Molecular Pediatrics, Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klaus Hamprecht
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany.
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8
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Herrmann L, Hahn F, Grau BW, Wild M, Niesar A, Wangen C, Kataev E, Marschall M, Tsogoeva SB. Autofluorescent Artemisinin-Benzimidazole Hybrids via Organo-Click Reaction: Study of Antiviral Properties and Mode of Action in Living Cells. Chemistry 2023; 29:e202301194. [PMID: 37267160 DOI: 10.1002/chem.202301194] [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: 04/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/04/2023]
Abstract
Drug modification by a fluorescent label is a common tool for studying its mechanism of action with fluorescence microscopy techniques. However, the attachment of a fluorescent label can significantly alter the polarity, solubility, and biological activity of the investigated drug, and, as a result, the studied mechanism of action can be misrepresented. Therefore, developing efficient drugs, which are inherently fluorescent and can be tracked directly in the cell is highly favorable. Here an easy formation of fluorescent hybrid drugs is presented, generated by a combination of two readily available non-fluorescent pharmacophores via a non-cleavable linker using a Ramachary-Bressy-Wang organocatalyzed azide-carbonyl [3+2] cycloaddition (organo-click) reaction. All newly prepared fluorescent compounds showed strong anti-HCMV activity (EC50 down to 0.07±0.00 μM), thus presenting a very promising drug developmental basis compared to the approved drug ganciclovir (EC50 2.60±0.50 μM). Remarkably, in vitro fluorescent imaging investigation of new compounds revealed induced changes in mitochondrial structures, which is a phenotypical hallmark of antiviral activity. This approach opens up new vistas for the easy formation of potent fluorescent drugs from readily available non-fluorescent parent compounds and might facilitate insight into their mode of action in living cells, avoiding the requirement of linkage to external fluorescent markers.
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Affiliation(s)
- Lars Herrmann
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg Department, Schlossgarten 4, 91054, Erlangen, Germany
| | - Benedikt W Grau
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Markus Wild
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg Department, Schlossgarten 4, 91054, Erlangen, Germany
| | - Aischa Niesar
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg Department, Schlossgarten 4, 91054, Erlangen, Germany
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg Department, Schlossgarten 4, 91054, Erlangen, Germany
| | - Evgeny Kataev
- Organic Chemistry Chair II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg Department, Schlossgarten 4, 91054, Erlangen, Germany
| | - Svetlana B Tsogoeva
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany
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9
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Liang J, Wu Y, Lan K, Dong C, Wu S, Li S, Zhou HB. Antiviral PROTACs: Opportunity borne with challenge. CELL INSIGHT 2023; 2:100092. [PMID: 37398636 PMCID: PMC10308200 DOI: 10.1016/j.cellin.2023.100092] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 07/04/2023]
Abstract
Proteolysis targeting chimera (PROTAC) degradation of pathogenic proteins by hijacking of the ubiquitin-proteasome-system has become a promising strategy in drug design. The overwhelming advantages of PROTAC technology have ensured a rapid and wide usage, and multiple PROTACs have entered clinical trials. Several antiviral PROTACs have been developed with promising bioactivities against various pathogenic viruses. However, the number of reported antiviral PROTACs is far less than that of other diseases, e.g., cancers, immune disorders, and neurodegenerative diseases, possibly because of the common deficiencies of PROTAC technology (e.g., limited available ligands and poor membrane permeability) plus the complex mechanism involved and the high tendency of viral mutation during transmission and replication, which may challenge the successful development of effective antiviral PROTACs. This review highlights the important advances in this rapidly growing field and critical limitations encountered in developing antiviral PROTACs by analyzing the current status and representative examples of antiviral PROTACs and other PROTAC-like antiviral agents. We also summarize and analyze the general principles and strategies for antiviral PROTAC design and optimization with the intent of indicating the potential strategic directions for future progress.
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Affiliation(s)
- Jinsen Liang
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Yihe Wu
- Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chune Dong
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shu Li
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Hai-Bing Zhou
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
- Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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10
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Li ZM, Liu G, Gao Y, Zhao MG. Targeting CDK7 in oncology: The avenue forward. Pharmacol Ther 2022; 240:108229. [PMID: 35700828 DOI: 10.1016/j.pharmthera.2022.108229] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 12/14/2022]
Abstract
Cyclin-dependent kinase (CDK) 7 is best characterized for the ability to regulate biological processes, including the cell cycle and gene transcription. Abnormal CDK7 activity is observed in various tumours and represents a driving force for tumourigenesis. Therefore, CDK7 may be an appealing target for cancer treatment. Whereas, the enthusiasm for CDK7-targeted therapeutic strategy is mitigated due to the widely possessed belief that this protein is essential for normal cells. Indeed, the fact confronts the consensus. This is the first review to introduce the role of CDK7 in pan-cancers via a combined analysis of comprehensive gene information and (pre)clinical research results. We also discuss the recent advances in protein structure and summarize the understanding of mechanisms underlying CDK7 function. These endeavours highlight the pivotal roles of CDK7 in tumours and may contribute to the development of effective CDK7 inhibitors within the strategy of structure-based drug discovery for cancer therapy.
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Affiliation(s)
- Zhi-Mei Li
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Guan Liu
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xinsi Road 1, Xi'an 710038, Shaanxi, PR China
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, Henan, PR China.
| | - Ming-Gao Zhao
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China; Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xinsi Road 1, Xi'an 710038, Shaanxi, PR China.
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11
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Friedl MS, Djakovic L, Kluge M, Hennig T, Whisnant AW, Backes S, Dölken L, Friedel CC. HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform. PLoS One 2022; 17:e0276467. [PMID: 36279270 PMCID: PMC9591066 DOI: 10.1371/journal.pone.0276467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
The herpes simplex virus 1 (HSV-1) virion host shut-off (vhs) protein cleaves both cellular and viral mRNAs by a translation-initiation-dependent mechanism, which should spare circular RNAs (circRNAs). Here, we show that vhs-mediated degradation of linear mRNAs leads to an enrichment of circRNAs relative to linear mRNAs during HSV-1 infection. This was also observed in influenza A virus (IAV) infection, likely due to degradation of linear host mRNAs mediated by the IAV PA-X protein and cap-snatching RNA-dependent RNA polymerase. For most circRNAs, enrichment was not due to increased circRNA synthesis but due to a general loss of linear RNAs. In contrast, biogenesis of a circRNA originating from the long isoform (NEAT1_2) of the nuclear paraspeckle assembly transcript 1 (NEAT1) was induced both in HSV-1 infection-in a vhs-independent manner-and in IAV infection. This was associated with induction of novel linear splicing of NEAT1_2 both within and downstream of the circRNA. NEAT1_2 forms a scaffold for paraspeckles, nuclear bodies located in the interchromatin space, must likely remain unspliced for paraspeckle assembly and is up-regulated in HSV-1 and IAV infection. We show that NEAT1_2 splicing and up-regulation can be induced by ectopic co-expression of the HSV-1 immediate-early proteins ICP22 and ICP27, potentially linking increased expression and splicing of NEAT1_2. To identify other conditions with NEAT1_2 splicing, we performed a large-scale screen of published RNA-seq data. This uncovered both induction of NEAT1_2 splicing and poly(A) read-through similar to HSV-1 and IAV infection in cancer cells upon inhibition or knockdown of CDK7 or the MED1 subunit of the Mediator complex phosphorylated by CDK7. In summary, our study reveals induction of novel circular and linear NEAT1_2 splicing isoforms as a common characteristic of HSV-1 and IAV infection and highlights a potential role of CDK7 in HSV-1 or IAV infection.
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Affiliation(s)
- Marie-Sophie Friedl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Simone Backes
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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12
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Clopper KC, Taatjes DJ. Chemical inhibitors of transcription-associated kinases. Curr Opin Chem Biol 2022; 70:102186. [PMID: 35926294 PMCID: PMC10676000 DOI: 10.1016/j.cbpa.2022.102186] [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: 05/22/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022]
Abstract
Transcription by RNA polymerase II (pol II) is regulated by kinases. In recent years, many selective and potent inhibitors of pol II transcription-associated kinases have been developed, and these molecules have advanced understanding of kinase function in mammalian cells. Here, we focus on chemical inhibitors of the transcription-associated kinases CDK7, CDK8, CDK9, CDK12, CDK13, and CDK19. We provide a brief overview of the function of these kinases and common activation mechanisms. We then highlight the advantages of kinase inhibitors compared with other basic research methods, and describe the caveats associated with non-selective compounds (e.g. flavopiridol). We conclude with strategies and recommendations for implementation of chemical inhibitors for experimental analysis of transcription-associated kinases.
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Affiliation(s)
- Kevin C Clopper
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA.
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13
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The Oligomeric Assemblies of Cytomegalovirus Core Nuclear Egress Proteins Are Associated with Host Kinases and Show Sensitivity to Antiviral Kinase Inhibitors. Viruses 2022; 14:v14051021. [PMID: 35632762 PMCID: PMC9146606 DOI: 10.3390/v14051021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
The nucleo-cytoplasmic capsid egress of herpesviruses is a unique regulated process that ensures the efficiency of viral replication and release. For human cytomegalovirus (HCMV), the core of the nuclear egress complex (NEC) consists of the pUL50–pUL53 heterodimer that is able to oligomerize and thus to build hexameric lattices. These structures determine capsid binding and multicomponent protein interaction including NEC-associated host factors. The underlying characteristic of the core NEC formation is based on the N-terminal hook structure of pUL53 that binds into an alpha-helical groove of pUL50, and is thus described as a hook-into-groove interaction. This central regulatory element has recently been validated as a target of antiviral strategies, and first NEC-targeted prototypes of inhibitory small molecules were reported by our previous study. Here, we further analyzed the oligomerization properties of the viral NEC through an approach of chemical protein cross-linking. Findings were as follows: (i) a cross-link approach demonstrated the oligomeric state of the HCMV core NEC using material from HCMV-infected or plasmid-transfected cells, (ii) a Western blot-based identification of NEC-associated kinases using the cross-linked multicomponent NECs was successful, and (iii) we demonstrated the NEC-inhibitory and antiviral activity of specific inhibitors directed to these target kinases. Combined, the results strongly underline the functional importance of the oligomerization of the HCMV-specific NEC that is both phosphorylation-dependent and sensitive to antiviral kinase inhibitors.
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14
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Wild M, Hahn F, Brückner N, Schütz M, Wangen C, Wagner S, Sommerer M, Strobl S, Marschall M. Cyclin-Dependent Kinases (CDKs) and the Human Cytomegalovirus-Encoded CDK Ortholog pUL97 Represent Highly Attractive Targets for Synergistic Drug Combinations. Int J Mol Sci 2022; 23:ijms23052493. [PMID: 35269635 PMCID: PMC8910733 DOI: 10.3390/ijms23052493] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a pathogenic human herpesvirus associated with serious, potentially life-threatening symptoms in the immunocompromised or immunonaïve host. The limitations encountered by antiviral therapy options currently available include a narrow panel of accessible targets, the induction of viral drug resistance as well as severe drug dosage-mediated side-effects. Improved drug-targeting strategies to resolve these issues are the focus of our investigations. In particular, pharmaceutical kinase inhibitors (PKIs), either directed to host kinases or directed to the viral protein kinase pUL97, have been considered to overcome these restrictions. Recently, we reported the identification of a synergistic combination of two PKIs directed to host cyclin-dependent kinase 7 (CDK7) and viral CDK ortholog pUL97. Here, we substantiate these findings with the following results: (i) true drug synergy was exhibited by various chemical classes of PKI pairs directed to pUL97 and CDK7; (ii) no putative amplification of cytotoxicity by these drug combinations was observed; (iii) a reduction in drug dosage levels for synergistic combinations was defined on a quantitative basis and compared to monotreatments; (iv) the quantities of target proteins CDK7 and pUL97 expressed in HCMV-infected cells were assessed by confocal imaging, indicating a strong down-modulation of CDK7 levels as a result of synergistic drug treatment; (v) the functional importance of these target kinases, both binding to cyclin H, was illustrated by assessing HCMV replication under the viral genomic deletion of ORF-UL97 or cellular cyclin knock-out; (vi) new combinations of HCMV-specific drug synergy were demonstrated for solely host-directed treatments using PKIs against CDK2, CDK7, CDK8 and/or CDK9 and (vii) a triple PKI combination provided further support for the synergy approach. With these combined findings, this study highlights the potential of therapeutic drug combinations of approved, developmental and preclinical PKIs for expanding future options for anti-HCMV therapy.
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Affiliation(s)
- Markus Wild
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
| | - Nadine Brückner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
| | - Martin Schütz
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
| | - Mona Sommerer
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
| | - Stefan Strobl
- 4SC AG/4SC Discovery GmbH, Fraunhoferstraße 22, 82152 Planegg-Martinsried, Germany;
- BioNTech SE, Am Klopferspitz 19a, 82152 Planegg-Martinsried, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (F.H.); (N.B.); (M.S.); (C.W.); (S.W.); (M.S.)
- Correspondence: ; Tel.: +49-9131-8526089
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15
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Control of Expression of Key Cell Cycle Enzymes Drives Cell Line-Specific Functions of CDK7 in Human PDAC Cells. Int J Mol Sci 2022; 23:ijms23020812. [PMID: 35054996 PMCID: PMC8775745 DOI: 10.3390/ijms23020812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/30/2021] [Accepted: 01/08/2022] [Indexed: 01/16/2023] Open
Abstract
Inhibition of the dual function cell cycle and transcription kinase CDK7 is known to affect the viability of cancer cells, but the mechanisms underlying cell line-specific growth control remain poorly understood. Here, we employed a previously developed, highly specific small molecule inhibitor that non-covalently blocks ATP binding to CDK7 (LDC4297) to study the mechanisms underlying cell line-specific growth using a panel of genetically heterogeneous human pancreatic tumor lines as model system. Although LDC4297 diminished both transcription rates and CDK T-loop phosphorylation in a comparable manner, some PDAC lines displayed significantly higher sensitivity than others. We focused our analyses on two well-responsive lines (Mia-Paca2 and Panc89) that, however, showed significant differences in their viability upon extended exposure to limiting LDC4297 concentrations. Biochemical and RNAseq analysis revealed striking differences in gene expression and cell cycle control. Especially the downregulation of a group of cell cycle control genes, among them CDK1/2 and CDC25A/C, correlated well to the observed viability differences in Panc89 versus Mia-Paca2 cells. A parallel downregulation of regulatory pathways supported the hypothesis of a feedforward programmatic effect of CDK7 inhibitors, eventually causing hypersensitivity of PDAC lines.
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16
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Schweininger J, Kriegel M, Häge S, Conrad M, Alkhashrom S, Lösing J, Weiler S, Tillmanns J, Egerer-Sieber C, Decker A, Lenac Roviš T, Eichler J, Sticht H, Marschall M, Muller YA. The crystal structure of the varicella-zoster Orf24-Orf27 nuclear egress complex spotlights multiple determinants of herpesvirus subfamily specificity. J Biol Chem 2022; 298:101625. [PMID: 35074430 PMCID: PMC8867122 DOI: 10.1016/j.jbc.2022.101625] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
Varicella-zoster virus (VZV) is a human pathogen from the α-subfamily of herpesviruses. The VZV Orf24-Orf27 complex represents the essential viral core nuclear egress complex (NEC) that orchestrates the egress of the preassembled virus capsids from the nucleus. While previous studies have primarily emphasized that the architecture of core NEC complexes is highly conserved among herpesviruses, the present report focuses on subfamily-specific structural and functional features that help explain the differences in the autologous versus nonautologous interaction patterns observed for NEC formation across herpesviruses. Here, we describe the crystal structure of the Orf24-Orf27 complex at 2.1 Å resolution. Coimmunoprecipitation and confocal imaging data show that Orf24-Orf27 complex formation displays some promiscuity in a herpesvirus subfamily-restricted manner. At the same time, analysis of thermodynamic parameters of NEC formation of three prototypical α-, β-, and γ herpesviruses, i.e., VZV, human cytomegalovirus (HCMV), and Epstein–Barr virus (EBV), revealed highly similar binding affinities for the autologous interaction with specific differences in enthalpy and entropy. Computational alanine scanning, structural comparisons, and mutational data highlight intermolecular interactions shared among α-herpesviruses that are clearly distinct from those seen in β- and γ-herpesviruses, including a salt bridge formed between Orf24-Arg167 and Orf27-Asp126. This interaction is located outside of the hook-into-groove interface and contributes significantly to the free energy of complex formation. Combined, these data explain distinct properties of specificity and permissivity so far observed in herpesviral NEC interactions. These findings will prove valuable in attempting to target multiple herpesvirus core NECs with selective or broad-acting drug candidates.
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17
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Hahn F, Hamilton ST, Wangen C, Wild M, Kicuntod J, Brückner N, Follett JEL, Herrmann L, Kheimar A, Kaufer BB, Rawlinson WD, Tsogoeva SB, Marschall M. Development of a PROTAC-Based Targeting Strategy Provides a Mechanistically Unique Mode of Anti-Cytomegalovirus Activity. Int J Mol Sci 2021; 22:12858. [PMID: 34884662 PMCID: PMC8657773 DOI: 10.3390/ijms222312858] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a major pathogenic herpesvirus that is prevalent worldwide and it is associated with a variety of clinical symptoms. Current antiviral therapy options do not fully satisfy the medical needs; thus, improved drug classes and drug-targeting strategies are required. In particular, host-directed antivirals, including pharmaceutical kinase inhibitors, might help improve the drug qualities. Here, we focused on utilizing PROteolysis TArgeting Chimeras (PROTACs), i.e., hetero-bifunctional molecules containing two elements, namely a target-binding molecule and a proteolysis-inducing element. Specifically, a PROTAC that was based on a cyclin-dependent kinase (CDK) inhibitor, i.e., CDK9-directed PROTAC THAL-SNS032, was analyzed and proved to possess strong anti-HCMV AD169-GFP activity, with values of EC50 of 0.030 µM and CC50 of 0.175 µM (SI of 5.8). Comparing the effect of THAL-SNS032 with its non-PROTAC counterpart SNS032, data indicated a 3.7-fold stronger anti-HCMV efficacy. This antiviral activity, as illustrated for further clinically relevant strains of human and murine CMVs, coincided with the mid-nanomolar concentration range necessary for a drug-induced degradation of the primary (CDK9) and secondary targets (CDK1, CDK2, CDK7). In addition, further antiviral activities were demonstrated, such as the inhibition of SARS-CoV-2 replication, whereas other investigated human viruses (i.e., varicella zoster virus, adenovirus type 2, and Zika virus) were found insensitive. Combined, the antiviral quality of this approach is seen in its (i) mechanistic uniqueness; (ii) future options of combinatorial drug treatment; (iii) potential broad-spectrum activity; and (iv) applicability in clinically relevant antiviral models. These novel data are discussed in light of the current achievements of anti-HCMV drug development.
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Affiliation(s)
- Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (M.W.); (J.K.); (N.B.)
| | - Stuart T. Hamilton
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, Schools of Women’s and Children’s Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (S.T.H.); (J.E.L.F.); (W.D.R.)
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (M.W.); (J.K.); (N.B.)
| | - Markus Wild
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (M.W.); (J.K.); (N.B.)
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (M.W.); (J.K.); (N.B.)
| | - Nadine Brückner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (M.W.); (J.K.); (N.B.)
| | - Jasmine E. L. Follett
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, Schools of Women’s and Children’s Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (S.T.H.); (J.E.L.F.); (W.D.R.)
| | - Lars Herrmann
- Institute of Organic Chemistry I, FAU, 91058 Erlangen, Germany; (L.H.); (S.B.T.)
| | - Ahmed Kheimar
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (A.K.); (B.B.K.)
| | - Benedikt B. Kaufer
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (A.K.); (B.B.K.)
| | - William D. Rawlinson
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, Schools of Women’s and Children’s Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (S.T.H.); (J.E.L.F.); (W.D.R.)
| | - Svetlana B. Tsogoeva
- Institute of Organic Chemistry I, FAU, 91058 Erlangen, Germany; (L.H.); (S.B.T.)
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (C.W.); (M.W.); (J.K.); (N.B.)
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18
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Bhurta D, Bharate SB. Analyzing the scaffold diversity of cyclin-dependent kinase inhibitors and revisiting the clinical and preclinical pipeline. Med Res Rev 2021; 42:654-709. [PMID: 34605036 DOI: 10.1002/med.21856] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 07/04/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022]
Abstract
Kinases have gained an important place in the list of vital therapeutic targets because of their overwhelming clinical success in the last two decades. Among various clinically validated kinases, the cyclin-dependent kinases (CDK) are one of the extensively studied drug targets for clinical development. Food and Drug Administration has approved three CDK inhibitors for therapeutic use, and at least 27 inhibitors are under active clinical development. In the last decade, research and development in this area took a rapid pace, and thus the analysis of scaffold diversity is essential for future drug design. Available reviews lack the systematic study and discussion on the scaffold diversity of CDK inhibitors. Herein we have reviewed and critically analyzed the chemical diversity present in the preclinical and clinical pipeline of CDK inhibitors. Our analysis has shown that although several scaffolds represent CDK inhibitors, only the amino-pyrimidine is a well-represented scaffold. The three-nitrogen framework of amino-pyrimidine is a fundamental hinge-binding unit. Further, we have discussed the selectivity aspects among CDKs, the clinical trial dose-limiting toxicities, and highlighted the most advanced clinical candidates. We also discuss the changing paradigm towards selective inhibitors and an overview of ATP-binding pockets of all druggable CDKs. We carefully analyzed the clinical pipeline to unravel the candidates that are currently under active clinical development. In addition to the plenty of dual CDK4/6 inhibitors, there are many selective CDK7, CDK9, and CDK8/19 inhibitors in the clinical pipeline.
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Affiliation(s)
- Deendyal Bhurta
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
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Wang Y, Peng J, Mi X, Yang M. p53-GSDME Elevation: A Path for CDK7 Inhibition to Suppress Breast Cancer Cell Survival. Front Mol Biosci 2021; 8:697457. [PMID: 34490348 PMCID: PMC8417410 DOI: 10.3389/fmolb.2021.697457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/21/2021] [Indexed: 11/30/2022] Open
Abstract
Higher cyclin-dependent kinase (CDK7) expression is a character of breast cancer and indicates poor prognosis. Inhibiting CDK7 exhibited effective cancer cell suppression which implies the potential of CDK7 inhibition to be a method for anti-cancer treatment. Our study aimed to explore a novel mechanism of CDK7 inhibition for suppressing breast cancer cell survival. Here, we proved inhibiting CDK7 repressed breast cancer cell proliferation and colony formation and increased the apoptotic cell rate, with p53 and GSDME protein level elevation. When p53 was suppressed in MCF-7 cells, the decline of GSDME expression and associated stronger proliferation and colony formation could be observed. Since downregulation of GSDME was of benefit to breast cancer cells, p53 inhibition blocked the elevation of GSDME induced by CDK7 inhibition and retrieved cells from the tumor suppressive effect of CDK7 inhibition. Therefore, CDK7 inhibition exerted a negative effect on breast cancer cell proliferation and colony formation in a p53–GSDME dependent manner. These results revealed the CDK7–p53–GSDME axis could be a pathway affecting breast cancer cell survival.
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Affiliation(s)
- Yueyuan Wang
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jingyu Peng
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xuguang Mi
- Tumor Biotherapy Center, Jilin Province People's Hospital, Changchun, China
| | - Ming Yang
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, China
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Methodological Development of a Multi-Readout Assay for the Assessment of Antiviral Drugs against SARS-CoV-2. PATHOGENS (BASEL, SWITZERLAND) 2021; 10:pathogens10091076. [PMID: 34578109 PMCID: PMC8466411 DOI: 10.3390/pathogens10091076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/30/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
Currently, human infections with the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) are accelerating the ongoing spread of the pandemic. Several innovative types of vaccines have already been developed, whereas effective options of antiviral treatments still await a scientific implementation. The development of novel anti-SARS-CoV-2 drug candidates demands skillful strategies and analysis systems. Promising results have been achieved with first generation direct-acting antivirals targeting the viral polymerase RdRp or the protease 3CLpro. Such recently approved or investigational drugs like remdesivir and GC376 represent a basis for further development and optimization. Here, we establish a multi-readout assay (MRA) system that enables the antiviral assessment and mechanistic characterization of novel test compounds, drug repurposing and combination treatments. Our SARS-CoV-2-specific MRA combines the quantitative measurement of several parameters of virus infection, such as the intracellular production of proteins and genomes, enzymatic activities and virion release, as well as the use of reporter systems. In this regard, the antiviral efficacy of remdesivir and GC376 has been investigated in human Caco-2 cells. The readouts included the use of spike- and double-strand RNA-specific monoclonal antibodies for in-cell fluorescence imaging, a newly generated recombinant SARS-CoV-2 reporter virus d6YFP, the novel 3CLpro-based FRET CFP::YFP and the previously reported FlipGFP reporter assays, as well as viral genome-specific RT-qPCR. The data produced by our MRA confirm the high antiviral potency of these two drugs in vitro. Combined, this MRA approach may be applied for broader analyses of SARS-CoV-2-specific antivirals, including compound screenings and the characterization of selected drug candidates.
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21
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Functional Relevance of the Interaction between Human Cyclins and the Cytomegalovirus-Encoded CDK-Like Protein Kinase pUL97. Viruses 2021; 13:v13071248. [PMID: 34198986 PMCID: PMC8310212 DOI: 10.3390/v13071248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
The replication of human cytomegalovirus (HCMV) is characterized by a complex network of virus–host interaction. This involves the regulatory viral protein kinase pUL97, which represents a viral cyclin-dependent kinase ortholog (vCDK) combining typical structural and functional features of host CDKs. Notably, pUL97 interacts with the three human cyclin types T1, H and B1, whereby the binding region of cyclin T1 and the region conferring oligomerization of pUL97 were both assigned to amino acids 231–280. Here, we addressed the question of whether recombinant HCMVs harboring deletions in this region were impaired in cyclin interaction, kinase functionality or viral replication. To this end, recombinant HCMVs were generated by traceless BACmid mutagenesis and were phenotypically characterized using a methodological platform based on qPCR, coimmunoprecipitation, in vitro kinase assay (IVKA), Phos-tag Western blot and confocal imaging analysis. Combined data illustrate the following: (i) infection kinetics of all three recombinant HCMVs, i.e., ORF-UL97 ∆231–255, ∆256–280 and ∆231–280, showed impaired replication efficiency compared to the wild type, amongst which the largest deletion exhibited the most pronounced defect; (ii) specifically, this mutant ∆231–280 showed a loss of interaction with cyclin T1, as demonstrated by CoIP and confocal imaging; (iii) IVKA and Phos-tag analyses revealed strongly affected kinase activity for ∆231–280, with strong impairment of both autophosphorylation and substrate phosphorylation, but less pronounced impairments for ∆231–255 and ∆256–280; and (iv) a bioinformatic assessment of the pUL97–cyclin T1 complex led to the refinement of our current binding model. Thus, the results provide initial evidence for the functional importance of the pUL97–cyclin interaction concerning kinase activity and viral replication fitness.
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22
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Functionally active cyclin-dependent kinase 9 is essential for porcine reproductive and respiratory syndrome virus subgenomic RNA synthesis. Mol Immunol 2021; 135:351-364. [PMID: 33990004 DOI: 10.1016/j.molimm.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9) is a key regulator of RNA-polymerase II and a candidate therapeutic target for various virus infections such as respiratory syncytial virus, herpes simplex virus, human adenovirus, human cytomegalovirus, hepatitis virus B, and human papillomavirus. We employed CDK9-IN-1, a selective CDK9 inhibitor, to investigate the role of CDK9 in porcine reproductive and respiratory syndrome virus (PRRSV) infection. CDK9-IN-1 dose-dependently reduced PRRSV replication without cytotoxicity in the infected cells. The antiviral activity of CDK9-IN-1 was further confirmed by evaluating the effects of lentivirus-mediated CDK9 knockdown or CDK9 overexpression on PRRSV infection. Briefly, the depletion of CDK9 significantly inhibited viral replication, while the overexpression of CDK9 promoted viral replication. PRRSV infection also enhanced the nuclear export of CDK9 without affecting CDK9 protein expression. Viral replication cycle analyses further revealed that functionally active CDK9 in the cytosol advanced viral subgenomic RNA synthesis. Collectively, our data illustrated that CDK9 was a new host factor that was involved in PRRSV subgenomic RNA synthesis, and CDK9 inhibitor, CDK9-IN-1 was a promising antiviral candidate for PRRSV infection.
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23
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Dodge MJ, MacNeil KM, Tessier TM, Weinberg JB, Mymryk JS. Emerging antiviral therapeutics for human adenovirus infection: Recent developments and novel strategies. Antiviral Res 2021; 188:105034. [PMID: 33577808 DOI: 10.1016/j.antiviral.2021.105034] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
Human adenoviruses (HAdV) are ubiquitous human pathogens that cause a significant burden of respiratory, ocular, and gastrointestinal illnesses. Although HAdV infections are generally self-limiting, pediatric and immunocompromised individuals are at particular risk for developing severe disease. Currently, no approved antiviral therapies specific to HAdV exist. Recent outbreaks underscore the need for effective antiviral agents to treat life-threatening infections. In this review we will focus on recent developments in search of potential therapeutic agents for controlling HAdV infections, with a focus on those targeting post-entry stages of the virus replicative cycle.
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Affiliation(s)
- Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jason B Weinberg
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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24
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Raghuvanshi R, Bharate SB. Recent Developments in the Use of Kinase Inhibitors for Management of Viral Infections. J Med Chem 2021; 65:893-921. [PMID: 33539089 DOI: 10.1021/acs.jmedchem.0c01467] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Kinases are a group of therapeutic targets involved in the progression of numerous diseases, including cancer, rheumatoid arthritis, Alzheimer's disease, and viral infections. The majority of approved antiviral agents are inhibitors of virus-specific targets that are encoded by individual viruses. These inhibitors are narrow-spectrum agents that can cause resistance development. Viruses are dependent on host cellular proteins, including kinases, for progression of their life-cycle. Thus, targeting kinases is an important therapeutic approach to discovering broad-spectrum antiviral agents. As there are a large number of FDA approved kinase inhibitors for various indications, their repurposing for viral infections is an attractive and time-sparing strategy. Many kinase inhibitors, including baricitinib, ruxolitinib, imatinib, tofacitinib, pacritinib, zanubrutinib, and ibrutinib, are under clinical investigation for COVID-19. Herein, we discuss FDA approved kinase inhibitors, along with a repertoire of clinical/preclinical stage kinase inhibitors that possess antiviral activity or are useful in the management of viral infections.
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Affiliation(s)
- Rinky Raghuvanshi
- Medicinal Chemistry Division,CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research, Ghaziabad 201002, India
| | - Sandip B Bharate
- Medicinal Chemistry Division,CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research, Ghaziabad 201002, India
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Abstract
Cyclin-dependent kinase 7 (CDK7), along with cyclin H and MAT1, forms the CDK-activating complex (CAK), which directs progression through the cell cycle via T-loop phosphorylation of cell cycle CDKs. CAK is also a component of the general transcription factor, TFIIH. CDK7-mediated phosphorylation of RNA polymerase II (Pol II) at active gene promoters permits transcription. Cell cycle dysregulation is an established hallmark of cancer, and aberrant control of transcriptional processes, through diverse mechanisms, is also common in many cancers. Furthermore, CDK7 levels are elevated in a number of cancer types and are associated with clinical outcomes, suggestive of greater dependence on CDK7 activity, compared with normal tissues. These findings identify CDK7 as a cancer therapeutic target, and several recent publications report selective CDK7 inhibitors (CDK7i) with activity against diverse cancer types. Preclinical studies have shown that CDK7i cause cell cycle arrest, apoptosis and repression of transcription, particularly of super-enhancer-associated genes in cancer, and have demonstrated their potential for overcoming resistance to cancer treatments. Moreover, combinations of CDK7i with other targeted cancer therapies, including BET inhibitors, BCL2 inhibitors and hormone therapies, have shown efficacy in model systems. Four CDK7i, ICEC0942 (CT7001), SY-1365, SY-5609 and LY3405105, have now progressed to Phase I/II clinical trials. Here we describe the work that has led to the development of selective CDK7i, the current status of the most advanced clinical candidates, and discuss their potential importance as cancer therapeutics, both as monotherapies and in combination settings. ClinicalTrials.gov Identifiers: NCT03363893; NCT03134638; NCT04247126; NCT03770494.
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26
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Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Mol Cell 2021; 81:830-844.e13. [PMID: 33453168 DOI: 10.1016/j.molcel.2020.12.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/14/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
The MYC oncoprotein globally affects the function of RNA polymerase II (RNAPII). The ability of MYC to promote transcription elongation depends on its ubiquitylation. Here, we show that MYC and PAF1c (polymerase II-associated factor 1 complex) interact directly and mutually enhance each other's association with active promoters. PAF1c is rapidly transferred from MYC onto RNAPII. This transfer is driven by the HUWE1 ubiquitin ligase and is required for MYC-dependent transcription elongation. MYC and HUWE1 promote histone H2B ubiquitylation, which alters chromatin structure both for transcription elongation and double-strand break repair. Consistently, MYC suppresses double-strand break accumulation in active genes in a strictly PAF1c-dependent manner. Depletion of PAF1c causes transcription-dependent accumulation of double-strand breaks, despite widespread repair-associated DNA synthesis. Our data show that the transfer of PAF1c from MYC onto RNAPII efficiently couples transcription elongation with double-strand break repair to maintain the genomic integrity of MYC-driven tumor cells.
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27
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Liang H, Du J, Elhassan RM, Hou X, Fang H. Recent progress in development of cyclin-dependent kinase 7 inhibitors for cancer therapy. Expert Opin Investig Drugs 2021; 30:61-76. [PMID: 33183110 DOI: 10.1080/13543784.2021.1850693] [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] [Indexed: 12/18/2022]
Abstract
Introduction: Cyclin-dependent kinase 7 (CDK7) is a part of the CDK-activating kinase family (CAK) which has a key role in the cell cycle and transcriptional regulation. Several lines of evidence suggest that CDK7 is a promising therapeutic target for cancer. CDK7 selective inhibitors such as SY-5609 and CT7001 are in clinical development. Areas covered: We explore the biology of CDK7 and its role in cancer and follow this with an evaluation of the preclinical and clinical progress of CDK7 inhibitors, and their potential in the clinic. We searched PubMed and ClinicalTrials to identify relevant data from the database inception to 14 October 2020. Expert opinion: CDK7 inhibitors are next generation therapeutics for cancer. However, there are still challenges which include selectively, side effects, and drug resistance. Nevertheless, with ongoing clinical development of these inhibitors and greater analysis of their target, CDK7 inhibitors will become a promising approach for treatment of cancer in the near future.
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Affiliation(s)
- Hanzhi Liang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Jintong Du
- Shandong Cancer Hospital and Institute, Shandong First Medical University , Jinan, Shandong, China
| | - Reham M Elhassan
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University , Jinan, Shandong, China
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28
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Wild M, Kicuntod J, Seyler L, Wangen C, Bertzbach LD, Conradie AM, Kaufer BB, Wagner S, Michel D, Eickhoff J, Tsogoeva SB, Bäuerle T, Hahn F, Marschall M. Combinatorial Drug Treatments Reveal Promising Anticytomegaloviral Profiles for Clinically Relevant Pharmaceutical Kinase Inhibitors (PKIs). Int J Mol Sci 2021; 22:ijms22020575. [PMID: 33430060 PMCID: PMC7826512 DOI: 10.3390/ijms22020575] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a human pathogenic herpesvirus associated with a variety of clinical symptoms. Current antiviral therapy is not always effective, so that improved drug classes and drug-targeting strategies are needed. Particularly host-directed antivirals, including pharmaceutical kinase inhibitors (PKIs), may help to overcome problems of drug resistance. Here, we focused on utilizing a selection of clinically relevant PKIs and determined their anticytomegaloviral efficacies. Particularly, PKIs directed to host or viral cyclin-dependent kinases, i.e., abemaciclib, LDC4297 and maribavir, exerted promising profiles against human and murine cytomegaloviruses. The anti-HCMV in vitro activity of the approved anti-cancer drug abemaciclib was confirmed in vivo using our luciferase-based murine cytomegalovirus (MCMV) animal model in immunocompetent mice. To assess drug combinations, we applied the Bliss independence checkerboard and Loewe additivity fixed-dose assays in parallel. Results revealed that (i) both affirmative approaches provided valuable information on anti-CMV drug efficacies and interactions, (ii) the analyzed combinations comprised additive, synergistic or antagonistic drug interactions consistent with the drugs’ antiviral mode-of-action, (iii) the selected PKIs, especially LDC4297, showed promising inhibitory profiles, not only against HCMV but also other α-, β- and γ-herpesviruses, and specifically, (iv) the combination treatment with LDC4297 and maribavir revealed a strong synergism against HCMV, which might open doors towards novel clinical options in the near future. Taken together, this study highlights the potential of therapeutic drug combinations of current developmental/preclinical PKIs.
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Affiliation(s)
- Markus Wild
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (J.K.); (C.W.); (S.W.); (F.H.)
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (J.K.); (C.W.); (S.W.); (F.H.)
| | - Lisa Seyler
- Institute of Radiology, University Medical Center Erlangen, FAU, Palmsanlage 5, 91054 Erlangen, Germany; (L.S.); (T.B.)
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (J.K.); (C.W.); (S.W.); (F.H.)
| | - Luca D. Bertzbach
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163 Berlin, Germany; (L.D.B.); (A.M.C.); (B.B.K.)
| | - Andelé M. Conradie
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163 Berlin, Germany; (L.D.B.); (A.M.C.); (B.B.K.)
| | - Benedikt B. Kaufer
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7-13, 14163 Berlin, Germany; (L.D.B.); (A.M.C.); (B.B.K.)
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (J.K.); (C.W.); (S.W.); (F.H.)
| | - Detlef Michel
- Institute for Virology, Ulm University Medical Center, Albert-Einstein-Allee 11, 89081 Ulm, Germany;
| | - Jan Eickhoff
- Lead Discovery Center GmbH, Otto-Hahn-Str. 15, 44227 Dortmund, Germany;
| | - Svetlana B. Tsogoeva
- Institute of Organic Chemistry I, FAU, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany;
| | - Tobias Bäuerle
- Institute of Radiology, University Medical Center Erlangen, FAU, Palmsanlage 5, 91054 Erlangen, Germany; (L.S.); (T.B.)
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (J.K.); (C.W.); (S.W.); (F.H.)
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany; (M.W.); (J.K.); (C.W.); (S.W.); (F.H.)
- Correspondence: ; Tel.: +49-9131-8526-089
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IMU-838, a Developmental DHODH Inhibitor in Phase II for Autoimmune Disease, Shows Anti-SARS-CoV-2 and Broad-Spectrum Antiviral Efficacy In Vitro. Viruses 2020; 12:v12121394. [PMID: 33291455 PMCID: PMC7762174 DOI: 10.3390/v12121394] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/17/2022] Open
Abstract
The ongoing pandemic spread of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) demands skillful strategies for novel drug development, drug repurposing and cotreatments, in particular focusing on existing candidates of host-directed antivirals (HDAs). The developmental drug IMU-838, currently being investigated in a phase 2b trial in patients suffering from autoimmune diseases, represents an inhibitor of human dihydroorotate dehydrogenase (DHODH) with a recently proven antiviral activity in vitro and in vivo. Here, we established an analysis system for assessing the antiviral potency of IMU-838 and DHODH-directed back-up drugs in cultured cell-based infection models. By the use of SARS-CoV-2-specific immunofluorescence, Western blot, in-cell ELISA, viral yield reduction and RT-qPCR methods, we demonstrated the following: (i) IMU-838 and back-ups show anti-SARS-CoV-2 activity at several levels of viral replication, i.e., protein production, double-strand RNA synthesis, and release of infectious virus; (ii) antiviral efficacy in Vero cells was demonstrated in a micromolar range (IMU-838 half-maximal effective concentration, EC50, of 7.6 ± 5.8 µM); (iii) anti-SARS-CoV-2 activity was distinct from cytotoxic effects (half-cytotoxic concentration, CC50, >100 µM); (iv) the drug in vitro potency was confirmed using several Vero lineages and human cells; (v) combination with remdesivir showed enhanced anti-SARS-CoV-2 activity; (vi) vidofludimus, the active determinant of IMU-838, exerted a broad-spectrum activity against a selection of major human pathogenic viruses. These findings strongly suggest that developmental DHODH inhibitors represent promising candidates for use as anti-SARS-CoV-2 therapeutics.
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30
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Nakayama S, Adachi M, Hatano M, Inahata N, Nagao T, Fukushima N. Cytosine arabinoside induces phosphorylation of histone H2AX in hippocampal neurons via a noncanonical pathway. Neurochem Int 2020; 142:104933. [PMID: 33290798 DOI: 10.1016/j.neuint.2020.104933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/29/2022]
Abstract
Cytosine arabinoside (Ara-C), an anticancer drug, is known to inhibit DNA replication in mitotic cells. Ara-C is also considered to induce DNA damage, leading to neuronal cell death. To identify the mechanism by which Ara-C kills neurons, we assessed the levels of phosphorylated histone H2AX (γ-H2AX), a marker for DNA double-strand breaks (DSBs), in hippocampal neurons cultured for 48 h with Ara-C. There was a time-dependent increase in the percentage of cells accumulating γ-H2AX, but TUNEL staining did not indicate the formation of DSBs. The nuclear spread of γ-H2AX remained after Ara-C was withdrawn. These features of Ara-C-induced γ-H2AX formation were quite distinct from those observed in proliferating pheochromocytoma cells. Furthermore, Ara-C-induced γ-H2AX formation appeared to utilize cyclin-dependent kinase 7, but not ataxia telangiectasia mutated (ATM) or ATM and Rad3 related, which are well-known kinases in γ-H2AX formation. Taken together, our findings indicated that Ara-C stimulated γ-H2AX formation in neurons without DSB formation and utilization of canonical kinases, leading to neuronal cell death.
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Affiliation(s)
- Saki Nakayama
- Department of Life Science, Kindai University, Higashiosaka, Japan
| | - Miyu Adachi
- Department of Life Science, Kindai University, Higashiosaka, Japan
| | - Misaki Hatano
- Department of Life Science, Kindai University, Higashiosaka, Japan
| | - Noriyuki Inahata
- Department of Life Science, Kindai University, Higashiosaka, Japan
| | - Tetsuji Nagao
- Department of Life Science, Kindai University, Higashiosaka, Japan
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31
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A review on kinases phosphorylating the carboxyl-terminal domain of RNA polymerase II-Biological functions and inhibitors. Bioorg Chem 2020; 104:104318. [PMID: 33142427 DOI: 10.1016/j.bioorg.2020.104318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/18/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (RNA Pol II) plays a major role in gene transcription for eukaryote. One of the major modes of regulation in eukaryotes is the phosphorylation of the carboxyl-terminal domain (CTD) of RNA Pol II. The current study found that the phosphorylation of Ser2, Ser5, Ser7, Thr4 and Tyr1 among the heptapeptide repeats of CTD plays a key role in the transcription process. We therefore review the biological functions and inhibitors of kinases that phosphorylate these amino acid residues including transcriptional cyclin-dependent protein kinases (CDKs), bromodomain-containing protein 4 (BRD4), Polo-like kinases 3 (Plk3) and Abelson murine leukemia viral oncogene 1 and 2 (c-Abl1/2).
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32
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Marschall M, Strojan H, Kiener R, Wangen C, Sonntag E, Müller R, Zeitträger I, Wagner S, Stamminger T, Milbradt J, Behrends U, Körber N, Bauer T, Schrödel S, Thirion C, Wagner R, Hutterer C. Differential upregulation of host cell protein kinases by the replication of α-, β- and γ-herpesviruses provides a signature of virus-specific signalling. J Gen Virol 2020; 101:284-289. [PMID: 31958050 DOI: 10.1099/jgv.0.001370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Infections with human herpesviruses share several molecular characteristics, but the diversified medical outcomes are distinct to viral subfamilies and species. Notably, both clinical and molecular correlates of infection are a challenging field and distinct patterns of virus-host interaction have rarely been defined; this study therefore focuses on the search for virus-specific molecular indicators. As previous studies have demonstrated the impact of herpesvirus infections on changes in host signalling pathways, we illustrate virus-modulated expression levels of individual cellular protein kinases. Current data reveal (i) α-, β- and γ-herpesvirus-specific patterns of kinase modulation as well as (ii) differential levels of up-/downregulated kinase expression and phosphorylation, which collectively suggest (iii) defined signalling patterns specific for the various viruses (VSS) that may prove useful for defining molecular indicators. Combined, the study confirms the correlation between herpesviral replication and modulation of signalling kinases, possibly exploitable for the in vitro characterization of viral infections.
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Affiliation(s)
- Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hanife Strojan
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Richard Kiener
- Institute for Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Eric Sonntag
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Regina Müller
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Isabel Zeitträger
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | - Jens Milbradt
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Uta Behrends
- German Center for Infection Research (DZIF), Munich, Germany
- Research Unit Gene Vectors, Helmholtz Zentrum München/TUM, Munich, Germany
- Children's Hospital Schwabing, Technische Universität München (TUM), Munich, Germany
| | - Nina Körber
- Institute of Virology, Helmholtz Zentrum München/TUM, Munich, Germany
| | - Tanja Bauer
- Institute of Virology, Helmholtz Zentrum München/TUM, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | | | | | - Ralf Wagner
- Institute for Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Corina Hutterer
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
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The Artemisinin-Derived Autofluorescent Compound BG95 Exerts Strong Anticytomegaloviral Activity Based on a Mitochondrial Targeting Mechanism. Int J Mol Sci 2020; 21:ijms21155578. [PMID: 32759737 PMCID: PMC7432203 DOI: 10.3390/ijms21155578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/05/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a major human pathogen associated with severe pathology. Current options of antiviral therapy only partly satisfy the needs of a well-tolerated long-term treatment/prophylaxis free from drug-induced viral resistance. Recently, we reported the strong antiviral properties in vitro and in vivo of the broad-spectrum anti-infective drug artesunate and its optimized derivatives. NF-κB signaling was described as a targeting mechanism and additional target proteins have recently been identified. Here, we analyzed the autofluorescent hybrid compound BG95, which could be utilized for intracellular visualization by confocal imaging and a tracking analysis in virus-infected primary human fibroblasts. As an important finding, BG95 accumulated in mitochondria visualized by anti-prohibitin and MitoTracker staining, and induced statistically significant changes of mitochondrial morphology, distinct from those induced by HCMV infection. Notably, mitochondrial membrane potential was found substantially reduced by BG95, an effect apparently counteracting efficient HCMV replication, which requires active mitochondria and upregulated energy levels. This finding was consistent with binding properties of artesunate-like compounds to mitochondrial proteins and thereby suggested a new mechanistic aspect. Combined, the present study underlines an important role of mitochondria in the multifaceted, host-directed antiviral mechanism of this drug class, postulating a new mitochondria-specific mode of protein targeting.
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Yiu SPT, Dorothea M, Hui KF, Chiang AKS. Lytic Induction Therapy against Epstein-Barr Virus-Associated Malignancies: Past, Present, and Future. Cancers (Basel) 2020; 12:cancers12082142. [PMID: 32748879 PMCID: PMC7465660 DOI: 10.3390/cancers12082142] [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: 06/29/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/29/2022] Open
Abstract
Epstein-Barr virus (EBV) lytic induction therapy is an emerging virus-targeted therapeutic approach that exploits the presence of EBV in tumor cells to confer specific killing effects against EBV-associated malignancies. Efforts have been made in the past years to uncover the mechanisms of EBV latent-lytic switch and discover different classes of chemical compounds that can reactivate the EBV lytic cycle. Despite the growing list of compounds showing potential to be used in the lytic induction therapy, only a few are being tested in clinical trials, with varying degrees of success. This review will summarize the current knowledge on EBV lytic reactivation, the major hurdles of translating the lytic induction therapy into clinical settings, and highlight some potential strategies in the future development of this therapy for EBV-related lymphoid and epithelial malignancies.
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Hahn F, Niesar A, Wangen C, Wild M, Grau B, Herrmann L, Capci A, Adrait A, Couté Y, Tsogoeva SB, Marschall M. Target verification of artesunate-related antiviral drugs: Assessing the role of mitochondrial and regulatory proteins by click chemistry and fluorescence labeling. Antiviral Res 2020; 180:104861. [PMID: 32590041 DOI: 10.1016/j.antiviral.2020.104861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 12/22/2022]
Abstract
Human cytomegalovirus (HCMV) infection is associated with serious pathology such as transplant rejection or embryonic developmental defects. Antiviral treatment with currently available drugs targeting viral enzymes is often accompanied with severe side effects and the occurrence of drug-resistant viruses. For this reason, novel ways of anti-HCMV therapy focusing on so far unexploited small molecules, targets and mechanisms are intensively studied. Recently, we described the pronounced antiviral activity of the artesunate-related class of trioxane compounds, comprising NF-κB/signaling inhibitors like the trimeric derivative TF27, which proved to be highly active in a nanomolar range both in vitro and in vivo. Here, we extend this analysis by presenting further TF27/artesunate-derived antiviral compounds designed for their specific use in target verification by click chemistry applied in fluorescence labeling and tag affinity strategies. Our main findings are as follows: (i) compounds TF27, BG95, AC98 and AC173 exert strong inhibitory activity against HCMV replication in cultured primary human cells, (ii) autofluorescence activity could be quantitatively detected for BG95 and AC98, and confocal fluorescence imaging revealed accumulation in mitochondria, (iii) postulated cellular targets including mitochondrial proteins were down-regulated upon TF27 treatment, (iv) a click chemistry-based protocol of target enrichment was established, and (v) mass spectrometry-based proteomic analysis, using proteins from HCMV-infected fibroblasts covalently interacting with AC173, revealed a refined list of targets. Combined, data strongly suggest a complex mode of antiviral drug-target interaction of artesunate-related compounds, now highlighting potential roles of mitochondrial, NF-κB pathway proteins, exportins and possibly more. This strategy may further promote antiviral drug development on the basis of pharmacologically optimized trioxane derivatives.
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Affiliation(s)
- Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Aischa Niesar
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Markus Wild
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Benedikt Grau
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Lars Herrmann
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Aysun Capci
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Annie Adrait
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, 38000, Grenoble, France.
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, 38000, Grenoble, France.
| | - Svetlana B Tsogoeva
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
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Abstract
Concerted multidisciplinary efforts have led to the development of Cyclin-Dependent Kinase inhibitors (CDKi’s) as small molecule drugs and chemical probes of intracellular CDK function. However, conflicting data has been reported on the inhibitory potency of CDKi’s and a systematic characterization of affinity and selectivity against intracellular CDKs is lacking. We have developed a panel of cell-permeable energy transfer probes to quantify target occupancy for all 21 human CDKs in live cells, and present a comprehensive evaluation of intracellular isozyme potency and selectivity for a collection of 46 clinically-advanced CDKi’s and tool molecules. We observed unexpected intracellular activity profiles for a number of CDKi’s, offering avenues for repurposing of highly potent molecules as probes for previously unreported targets. Overall, we provide a broadly applicable method for evaluating the selectivity of CDK inhibitors in living cells, and present a refined set of tool molecules to study CDK function. Cyclin-dependent kinase (CDK) inhibitors are widely used both in the clinic and for basic research aimed at dissecting the specific cellular functions of specific CDKs. Here, the authors report the development of a panel of fluorescent reporter probes and provide a comprehensive profile of the inhibitory activity of several CDK inhibitors towards all 21 CDKs in living cells.
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Abstract
Antiviral drugs have traditionally been developed by directly targeting essential viral components. However, this strategy often fails due to the rapid generation of drug-resistant viruses. Recent genome-wide approaches, such as those employing small interfering RNA (siRNA) or clustered regularly interspaced short palindromic repeats (CRISPR) or those using small molecule chemical inhibitors targeting the cellular "kinome," have been used successfully to identify cellular factors that can support virus replication. Since some of these cellular factors are critical for virus replication, but are dispensable for the host, they can serve as novel targets for antiviral drug development. In addition, potentiation of immune responses, regulation of cytokine storms, and modulation of epigenetic changes upon virus infections are also feasible approaches to control infections. Because it is less likely that viruses will mutate to replace missing cellular functions, the chance of generating drug-resistant mutants with host-targeted inhibitor approaches is minimized. However, drug resistance against some host-directed agents can, in fact, occur under certain circumstances, such as long-term selection pressure of a host-directed antiviral agent that can allow the virus the opportunity to adapt to use an alternate host factor or to alter its affinity toward the target that confers resistance. This review describes novel approaches for antiviral drug development with a focus on host-directed therapies and the potential mechanisms that may account for the acquisition of antiviral drug resistance against host-directed agents.
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Abstract
Cyclin-dependent kinase 7 (CDK7) plays crucial roles in the regulation of cell cycle and transcription that are tightly associated with cancer development and metastasis. The recent identification of the first covalent inhibitor which possesses high specificity against CDK7 prompts intense studies on designing highly selective CDK7 inhibitors and exploring their applications in cancer treatments. This review summarizes the latest biological studies on CDK7 and reviews the development of CDK7 inhibitors in preclinical and clinical evaluations, along with the prospects and potential challenges in this research area. CDK7 is an attractive anticancer target, and the discovery and development of CDK7 inhibitors has received much attention.
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Diab S, Yu M, Wang S. CDK7 Inhibitors in Cancer Therapy: The Sweet Smell of Success? J Med Chem 2020; 63:7458-7474. [DOI: 10.1021/acs.jmedchem.9b01985] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sarah Diab
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Mingfeng Yu
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, University of South Australia Cancer Research Institute, Adelaide, SA 5000, Australia
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Adamson CS, Nevels MM. Bright and Early: Inhibiting Human Cytomegalovirus by Targeting Major Immediate-Early Gene Expression or Protein Function. Viruses 2020; 12:v12010110. [PMID: 31963209 PMCID: PMC7019229 DOI: 10.3390/v12010110] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
The human cytomegalovirus (HCMV), one of eight human herpesviruses, establishes lifelong latent infections in most people worldwide. Primary or reactivated HCMV infections cause severe disease in immunosuppressed patients and congenital defects in children. There is no vaccine for HCMV, and the currently approved antivirals come with major limitations. Most approved HCMV antivirals target late molecular processes in the viral replication cycle including DNA replication and packaging. “Bright and early” events in HCMV infection have not been exploited for systemic prevention or treatment of disease. Initiation of HCMV replication depends on transcription from the viral major immediate-early (IE) gene. Alternative transcripts produced from this gene give rise to the IE1 and IE2 families of viral proteins, which localize to the host cell nucleus. The IE1 and IE2 proteins are believed to control all subsequent early and late events in HCMV replication, including reactivation from latency, in part by antagonizing intrinsic and innate immune responses. Here we provide an update on the regulation of major IE gene expression and the functions of IE1 and IE2 proteins. We will relate this insight to experimental approaches that target IE gene expression or protein function via molecular gene silencing and editing or small chemical inhibitors.
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41
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Recent advances in the development of cyclin-dependent kinase 7 inhibitors. Eur J Med Chem 2019; 183:111641. [DOI: 10.1016/j.ejmech.2019.111641] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
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A high-throughput screen identifies that CDK7 activates glucose consumption in lung cancer cells. Nat Commun 2019; 10:5444. [PMID: 31784510 PMCID: PMC6884612 DOI: 10.1038/s41467-019-13334-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
Elevated glucose consumption is fundamental to cancer, but selectively targeting this pathway is challenging. We develop a high-throughput assay for measuring glucose consumption and use it to screen non-small-cell lung cancer cell lines against bioactive small molecules. We identify Milciclib that blocks glucose consumption in H460 and H1975, but not in HCC827 or A549 cells, by decreasing SLC2A1 (GLUT1) mRNA and protein levels and by inhibiting glucose transport. Milciclib blocks glucose consumption by targeting cyclin-dependent kinase 7 (CDK7) similar to other CDK7 inhibitors including THZ1 and LDC4297. Enhanced PIK3CA signaling leads to CDK7 phosphorylation, which promotes RNA Polymerase II phosphorylation and transcription. Milciclib, THZ1, and LDC4297 lead to a reduction in RNA Polymerase II phosphorylation on the SLC2A1 promoter. These data indicate that our high-throughput assay can identify compounds that regulate glucose consumption and that CDK7 is a key regulator of glucose consumption in cells with an activated PI3K pathway. Many cancer cells have increased glucose consumption compared to normal cells, a feature that can be exploited therapeutically. Here, the authors carry out a chemical screen and identify compounds that selectively blocks glucose metabolism in non-small-cell lung cancer cell lines.
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43
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Shen S, Dean DC, Yu Z, Duan Z. Role of cyclin-dependent kinases (CDKs) in hepatocellular carcinoma: Therapeutic potential of targeting the CDK signaling pathway. Hepatol Res 2019; 49:1097-1108. [PMID: 31009153 DOI: 10.1111/hepr.13353] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 02/23/2019] [Accepted: 03/28/2019] [Indexed: 12/12/2022]
Abstract
Liver cancer is the fourth leading cause of cancer related mortality in the world, with hepatocellular carcinoma (HCC) representing the most common primary subtype. Two-thirds of HCC patients have advanced disease when diagnosed, and for these patients, treatment strategies remain limited. In addition, there is a high incidence of tumor recurrence after surgical resection with the current treatment regimens. The development of novel and more effective agents is required. Cyclin-dependent kinases (CDKs) constitute a family of 21 different protein kinases involved in regulating cell proliferation, apoptosis, and drug resistance, and are evaluated in preclinical and clinical trials as chemotherapeutics. To summarize and discuss the therapeutic potential of targeting CDKs in HCC, recent published articles identified from PubMed were comprehensively reviewed. The key words included hepatocellular carcinoma, cyclin-dependent kinases, and CDK inhibitors. This review focuses on the emerging evidence from studies describing the genetic and functional aspects of CDKs in HCC. We also present an overview of CDK inhibitors that have shown efficacy in laboratory studies of HCC. Although many of the studies assessing CDK-targeting therapies in HCC are at the preclinical stage, there is significant evidence that CDK inhibitors used alone or in combination with established chemotherapy drugs could have significant applications in HCC.
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Affiliation(s)
- Shen Shen
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Sarcoma Biology Laboratory, Department of Orthopedic Surgery, David Geffen School of Medicine at University of Los Angeles, Los Angeles, CA, USA
| | - Dylan C Dean
- Sarcoma Biology Laboratory, Department of Orthopedic Surgery, David Geffen School of Medicine at University of Los Angeles, Los Angeles, CA, USA
| | - Zujiang Yu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenfeng Duan
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Sarcoma Biology Laboratory, Department of Orthopedic Surgery, David Geffen School of Medicine at University of Los Angeles, Los Angeles, CA, USA
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Wold WSM, Tollefson AE, Ying B, Spencer JF, Toth K. Drug development against human adenoviruses and its advancement by Syrian hamster models. FEMS Microbiol Rev 2019; 43:380-388. [PMID: 30916746 DOI: 10.1093/femsre/fuz008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/25/2019] [Indexed: 02/02/2023] Open
Abstract
The symptoms of human adenovirus infections are generally mild and self-limiting. However, these infections have been gaining importance in recent years because of a growing number of immunocompromised patients. Solid organ and hematopoietic stem cell transplant patients are subjected to severe immunosuppressive regimes and cannot efficaciously eliminate virus infections. In these patients, adenovirus infections can develop into deadly multi-organ disseminated disease. Presently, in the absence of approved therapies, physicians rely on drugs developed for other purposes to treat adenovirus infections. As there is a need for anti-adenoviral therapies, researchers have been developing new agents and repurposing existing ones to treat adenovirus infections. There are several small molecule drugs that are being tested for their efficacy against human adenoviruses; some of these have reached clinical trials, while others are still in the preclinical phase. Besides these compounds, research on immunotherapy against adenoviral infection has made significant progress, promising another modality for treatment. The availability of an animal model confirmed the activity of some drugs already in clinical use while proving that others are inactive. This led to the identification of several lead compounds that await further development. In the present article, we review the current status of anti-adenoviral therapies and their advancement by in vivo studies in the Syrian hamster model.
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Affiliation(s)
- William S M Wold
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO, USA
| | - Ann E Tollefson
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO, USA
| | - Baoling Ying
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO, USA
| | - Jacqueline F Spencer
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO, USA
| | - Karoly Toth
- Saint Louis University School of Medicine, Department of Molecular Microbiology and Immunology, 1100 S. Grand Boulevard, St. Louis, MO, USA
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45
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Sahoo CR, Paidesetty SK, Padhy RN. Nornostocine congeners as potential anticancer drugs: An overview. Drug Dev Res 2019. [DOI: 10.1002/ddr.21577] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Chita R. Sahoo
- Central Research Laboratory, Institute of Medical Sciences & Sum HospitalSiksha ‘O’ Anusandhan (Deemed to be University) Bhubaneswar Odisha India
- Department of Medicinal Chemistry, School of Pharmaceutical SciencesSiksha ‘O’ Anusandhan (Deemed to be University) Bhubaneswar Odisha India
| | - Sudhir K. Paidesetty
- Department of Medicinal Chemistry, School of Pharmaceutical SciencesSiksha ‘O’ Anusandhan (Deemed to be University) Bhubaneswar Odisha India
| | - Rabindra N. Padhy
- Central Research Laboratory, Institute of Medical Sciences & Sum HospitalSiksha ‘O’ Anusandhan (Deemed to be University) Bhubaneswar Odisha India
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46
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Efficacy of the novel CDK7 inhibitor QS1189 in mantle cell lymphoma. Sci Rep 2019; 9:7193. [PMID: 31076643 PMCID: PMC6510728 DOI: 10.1038/s41598-019-43760-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/14/2019] [Indexed: 01/05/2023] Open
Abstract
Mantle cell lymphoma (MCL) is typically an aggressive and rare form of non-Hodgkin lymphoma (NHL) with a poor prognosis despite recent advances in immunochemotherapy and targeted therapeutics against NHL. New therapeutic agents are needed for MCL. In this study, we generated a potent inhibitor of cyclin-dependent kinase 7 (CDK7), designated QS1189, and confirmed its anti-cancer effects towards MCL and other lymphomas. QS1189 was highly selective for CDK7 and showed potent anticancer effects in MCL compared to other targeted therapeutic agents, such as ibrutinib and venetoclax. Consistent with a conventional CDK7 inhibitor, QS1189 treatment significantly decreased phosphorylation of the carboxyl-terminal domain of RNA polymerase II and transcription-associated genes. QS1189 induced cell cycle arrest at the G2/M phase and apoptosis. Interestingly, QS1189 overcame the acquired resistance to venetoclax, which is mediated by Bcl-xL. Similarly, QS1189 showed potent tumour cell growth inhibition of various lymphomas. Thus, CDK7 might be a suitable therapeutic target for inhibiting lymphoma, and QS1189 is a promising therapeutic option for various lymphomas and cells with acquired resistance to targeted therapy.
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47
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A synthesis of new 7-amino-substituted 4-aminopyrazolo[1,5-a][1,3,5]triazines via a selective three-component triazine ring annulation. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Steingruber M, Keller L, Socher E, Ferre S, Hesse AM, Couté Y, Hahn F, Büscher N, Plachter B, Sticht H, Marschall M. Cyclins B1, T1, and H differ in their molecular mode of interaction with cytomegalovirus protein kinase pUL97. J Biol Chem 2019; 294:6188-6203. [PMID: 30782840 DOI: 10.1074/jbc.ra118.007049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/08/2019] [Indexed: 12/19/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a common β-herpesvirus causing life-long latent infections. HCMV replication interferes with cell cycle regulation in host cells because the HCMV-encoded cyclin-dependent kinase (CDK) ortholog pUL97 extensively phosphorylates the checkpoint regulator retinoblastoma protein. pUL97 also interacts with cyclins B1, T1, and H, and recent findings have strongly suggested that these interactions influence pUL97 substrate recognition. Interestingly, here we detected profound mechanistic differences among these pUL97-cyclin interactions. Our study revealed the following. (i) pUL97 interacts with cyclins B1 and H in a manner dependent on pUL97 activity and HCMV-specific cyclin modulation, respectively. (ii) The phosphorylated state of both proteins is an important determinant of the pUL97-cyclin B1 interaction. (iii) Activated phospho-Thr-315 cyclin H is up-regulated during HCMV replication. (iv) Thr-315 phosphorylation is independent of intracellular pUL97 or CDK7 activity. (v) pUL97-mediated in vitro phosphorylation is detectable for cyclin B1 but not H. (vi) Mutual transphosphorylation between pUL97 and CDK7 is not detectable, and an MS-based phosphosite analysis indicated that pUL97 might unexpectedly not be phosphorylated in its T-loop. (vii) The binary complexes pUL97-cyclin H and CDK7-cyclin H as well as the ternary complex pUL97-cyclin-H-CDK7 are detectable in an assembly-based CoIP approach. (viii) pUL97 self-interaction can be bridged by the transcriptional cyclins T1 or H but not by the classical cell cycle-regulating B1 cyclin. Combined, our findings unravel a number of cyclin type-specific differences in pUL97 interactions and suggest a multifaceted regulatory impact of cyclins on HCMV replication.
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Affiliation(s)
- Mirjam Steingruber
- From the Institute for Clinical and Molecular Virology, 91054 Erlangen, Germany.
| | - Lena Keller
- From the Institute for Clinical and Molecular Virology, 91054 Erlangen, Germany
| | - Eileen Socher
- Division of Bioinformatics, Institute of Biochemistry Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sabrina Ferre
- the Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Anne-Marie Hesse
- the Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Yohann Couté
- the Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Friedrich Hahn
- From the Institute for Clinical and Molecular Virology, 91054 Erlangen, Germany
| | - Nicole Büscher
- the Institute for Virology, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Bodo Plachter
- the Institute for Virology, University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany.
| | - Manfred Marschall
- From the Institute for Clinical and Molecular Virology, 91054 Erlangen, Germany.
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49
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Cheng W, Yang Z, Wang S, Li Y, Wei H, Tian X, Kan Q. Recent development of CDK inhibitors: An overview of CDK/inhibitor co-crystal structures. Eur J Med Chem 2019; 164:615-639. [PMID: 30639897 DOI: 10.1016/j.ejmech.2019.01.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
The cyclin-dependent protein kinases (CDKs) are protein-serine/threonine kinases that display crucial effects in regulation of cell cycle and transcription. While the excessive expression of CDKs is intimate related to the development of diseases including cancers, which provides opportunities for disease treatment. A large number of small molecules are explored targeting CDKs. CDK/inhibitor co-crystal structures play an important role during the exploration of inhibitors. So far nine kinds of CDK/inhibitor co-crystals have been determined, they account for the highest proportion among the Protein Data Bank (PDB) deposited crystal structures. Herein, we review main co-crystals of CDKs in complex with corresponding inhibitors reported in recent years, focusing our attention on the binding models and the pharmacological activities of inhibitors.
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Affiliation(s)
- Weiyan Cheng
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhiheng Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Suhua Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ying Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Han Wei
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Quancheng Kan
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
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In vivo proof-of-concept for two experimental antiviral drugs, both directed to cellular targets, using a murine cytomegalovirus model. Antiviral Res 2018; 161:63-69. [PMID: 30452929 DOI: 10.1016/j.antiviral.2018.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022]
Abstract
Infections with the human cytomegalovirus (HCMV) cause serious medical problems including organ rejection and congenital infection. Treatment of HCMV infections with currently available medication targeting viral enzymes is often accompanied with severe side effects and the occurrence of drug-resistant viruses. This demands novel therapeutical approaches like targeting genetically stable host cell proteins that are crucial for virus replication. Although numerous experimental drugs with promising in vitro efficacy have been identified, the lack of available data in animal models limits their potential for further clinical development. Recently, we described the very strong in vitro antiherpesviral activity of the NF-κB inhibitor TF27 and the CDK7 inhibitor LDC4297 at low nanomolar concentrations. In the present study, we present first data for the in vivo efficacy of both experimental drugs using an established cytomegalovirus animal model (murine CMV replication in immunodefective Rag -/- mice). The main findings of this study are (i) a strong inhibitory potency against beta- and gamma-herpesviruses of both compounds in vitro, (ii) even more important, a pronounced anticytomegaloviral activity also exerted in vivo, that resulted from (iii) a restriction of viral replication to the site of infection, thus preventing organ dissemination, (iv) in the absence of major compound-associated adverse events. Thus, we provide evidence for a strong antiviral potency in vivo and proof-of-concept for both drugs, which may encourage their further drug development, possibly including pharmacologically optimized derivatives, for a potential use in future antiherpesviral treatment.
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