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Du S, Liu X, Hu X, Zhan P. Viral Protein Dimerization Quality Control: A Design Strategy for a Potential Viral Inhibitor. J Med Chem 2024. [PMID: 39303015 DOI: 10.1021/acs.jmedchem.4c01540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The global pharmaceutical market has been profoundly impacted by the coronavirus pandemic, leading to an increased demand for specific drugs. Consequently, drug resistance has prompted continuous innovation in drug design strategies to effectively combat resistant pathogens or disease variants. Protein dimers play crucial roles in vivo, including catalytic reactions, signal transduction, and structural stability. The site of action for protein dimerization modulators typically does not reside within the active site of the protein, thereby potentially impeding resistance development. Therefore, harnessing viral protein dimerization modulators could represent a promising avenue for combating viral infections. In this Perspective, we provide a detailed introduction to the design principles and applications of dimerization modulators in antiviral research. Furthermore, we analyze various representative examples to elucidate their modes of action while presenting our perspective on dimerization modulators along with the opportunities and challenges associated with this groundbreaking area of investigation.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
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2
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Prabaharan C, Figiel M, Szczepanowski RH, Skowronek K, Zajko W, Thangaraj V, Chamera S, Nowak E, Nowotny M. Structural and biochemical characterization of cauliflower mosaic virus reverse transcriptase. J Biol Chem 2024; 300:107555. [PMID: 39002684 PMCID: PMC11363490 DOI: 10.1016/j.jbc.2024.107555] [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: 12/01/2023] [Revised: 06/19/2024] [Accepted: 06/30/2024] [Indexed: 07/15/2024] Open
Abstract
Reverse transcriptases (RTs) are enzymes with DNA polymerase and RNase H activities. They convert ssRNA into dsDNA and are key enzymes for the replication of retroviruses and retroelements. Caulimoviridae is a major family of plant-infecting viruses. Caulimoviruses have a circular dsDNA genome that is replicated by reverse transcription, but in contrast to retroviruses, they lack integrase. Caulimoviruses are related to Ty3 retroelements. Ty3 RT has been extensively studied structurally and biochemically, but corresponding information for caulimoviral RTs is unavailable. In the present study, we report the first crystal structure of cauliflower mosaic virus (CaMV) RT in complex with a duplex made of RNA and DNA strands (RNA/DNA hybrid). CaMV RT forms a monomeric complex with the hybrid, unlike Ty3 RT, which does so as a dimer. Results of the RNA-dependent DNA polymerase and DNA-dependent DNA polymerase activity assays showed that individual CaMV RT molecules are able to perform full polymerase functions. However, our analyses showed that an additional CaMV RT molecule needs to transiently associate with a polymerase-competent RT molecule to execute RNase H cuts of the RNA strand. Collectively, our results provide details into the structure and function of CaMV RT and describe how the enzyme compares to other related RTs.
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Affiliation(s)
- Chandrasekaran Prabaharan
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Roman H Szczepanowski
- Biophysics and Bioanalytics Facility, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Krzysztof Skowronek
- Biophysics and Bioanalytics Facility, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vinuchakkaravarthy Thangaraj
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Sebastian Chamera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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3
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Arribas L, Menéndez-Arias L, Betancor G. May I Help You with Your Coat? HIV-1 Capsid Uncoating and Reverse Transcription. Int J Mol Sci 2024; 25:7167. [PMID: 39000271 PMCID: PMC11241228 DOI: 10.3390/ijms25137167] [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: 06/06/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) capsid is a protein core formed by multiple copies of the viral capsid (CA) protein. Inside the capsid, HIV-1 harbours all the viral components required for replication, including the genomic RNA and viral enzymes reverse transcriptase (RT) and integrase (IN). Upon infection, the RT transforms the genomic RNA into a double-stranded DNA molecule that is subsequently integrated into the host chromosome by IN. For this to happen, the viral capsid must open and release the viral DNA, in a process known as uncoating. Capsid plays a key role during the initial stages of HIV-1 replication; therefore, its stability is intimately related to infection efficiency, and untimely uncoating results in reverse transcription defects. How and where uncoating takes place and its relationship with reverse transcription is not fully understood, but the recent development of novel biochemical and cellular approaches has provided unprecedented detail on these processes. In this review, we present the latest findings on the intricate link between capsid stability, reverse transcription and uncoating, the different models proposed over the years for capsid uncoating, and the role played by other cellular factors on these processes.
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Affiliation(s)
- Laura Arribas
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain;
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), 28049 Madrid, Spain;
| | - Gilberto Betancor
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain;
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Maio N, Heffner AL, Rouault TA. Iron‑sulfur clusters in viral proteins: Exploring their elusive nature, roles and new avenues for targeting infections. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119723. [PMID: 38599324 PMCID: PMC11139609 DOI: 10.1016/j.bbamcr.2024.119723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Viruses have evolved complex mechanisms to exploit host factors for replication and assembly. In response, host cells have developed strategies to block viruses, engaging in a continuous co-evolutionary battle. This dynamic interaction often revolves around the competition for essential resources necessary for both host cell and virus replication. Notably, iron, required for the biosynthesis of several cofactors, including iron‑sulfur (FeS) clusters, represents a critical element in the ongoing competition for resources between infectious agents and host. Although several recent studies have identified FeS cofactors at the core of virus replication machineries, our understanding of their specific roles and the cellular processes responsible for their incorporation into viral proteins remains limited. This review aims to consolidate our current knowledge of viral components that have been characterized as FeS proteins and elucidate how viruses harness these versatile cofactors to their benefit. Its objective is also to propose that viruses may depend on incorporation of FeS cofactors more extensively than is currently known. This has the potential to revolutionize our understanding of viral replication, thereby carrying significant implications for the development of strategies to target infections.
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Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
| | - Audrey L Heffner
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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Palazzotti D, Sguilla M, Manfroni G, Cecchetti V, Astolfi A, Barreca ML. Small Molecule Drugs Targeting Viral Polymerases. Pharmaceuticals (Basel) 2024; 17:661. [PMID: 38794231 PMCID: PMC11124969 DOI: 10.3390/ph17050661] [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: 04/18/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Small molecules that specifically target viral polymerases-crucial enzymes governing viral genome transcription and replication-play a pivotal role in combating viral infections. Presently, approved polymerase inhibitors cover nine human viruses, spanning both DNA and RNA viruses. This review provides a comprehensive analysis of these licensed drugs, encompassing nucleoside/nucleotide inhibitors (NIs), non-nucleoside inhibitors (NNIs), and mutagenic agents. For each compound, we describe the specific targeted virus and related polymerase enzyme, the mechanism of action, and the relevant bioactivity data. This wealth of information serves as a valuable resource for researchers actively engaged in antiviral drug discovery efforts, offering a complete overview of established strategies as well as insights for shaping the development of next-generation antiviral therapeutics.
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Affiliation(s)
| | | | | | | | | | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy; (D.P.); (M.S.); (G.M.); (V.C.); (A.A.)
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Bai Y, Xi Y, He X, Twumasi G, Ma S, Tao Q, Xu M, Jiang S, Zhang T, Lu Y, Han X, Qi J, Li L, Bai L, Liu H. Genome-wide characterization and comparison of endogenous retroviruses among 3 duck reference genomes. Poult Sci 2024; 103:103543. [PMID: 38447307 PMCID: PMC11067759 DOI: 10.1016/j.psj.2024.103543] [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: 11/21/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
Endogenous retroviruses (ERV) are viral genomes integrated into the host genome and can be stably inherited. Although ERV sequences have been reported in some avian species' genome, the duck endogenous retroviruses (DERV) genome has yet to be quantified. This study aimed to identify ERV sequences and characterize genes near ERVs in the duck genome by utilizing LTRhavest and LTRdigest tools to forecast the duck genome and analyze the distribution of ERV copies. The results revealed 1,607, 2,031, and 1,908 full-length ERV copies in the Pekin duck (ZJU1.0), Mallard (CAU_wild_1.0), and Shaoxing duck (CAU_laying_1.0) genomes, respectively, with average lengths of 7,046, 7,027, and 6,945 bp. ERVs are mainly distributed on the 1, 2, and sex chromosomes. Phylogenetic analysis demonstrated the presence of Betaretrovirus in 3 duck genomes, whereas Alpharetrovirus was exclusively identified in the Shaoxing duck genome. Through screening, 596, 315, and 343 genes adjacent to ERV were identified in 3 duck genomes, respectively, and their functions of ERV neighboring genes were predicted. Functional enrichment analysis of ERV-adjacent genes revealed enrichment for Focal adhesion, Calcium signaling pathway, and Adherens junction in 3 duck genomes. The overlapped genes were highly expressed in 8 tissues (brain, fat, heart, kidney, liver, lung, skin, and spleen) of 8-wk-old Mallard, revealing their important expression in different tissues. Our study provides a new perspective for understanding the quantity and function of DERVs, and may also provide important clues for regulating nearby genes and affecting the traits of organisms.
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Affiliation(s)
- Yuan Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Yang Xi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Xinxin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Grace Twumasi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Shengchao Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Qiuyu Tao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Mengru Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Shuaixue Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Tao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Yinjuan Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Xu Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Jingjing Qi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Lili Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Hehe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China.
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Martínez Del Río J, López-Carrobles N, Mendieta-Moreno JI, Herrera-Chacón Ó, Sánchez-Ibáñez A, Mendieta J, Menéndez-Arias L. Charge Engineering of the Nucleic Acid Binding Cleft of a Thermostable HIV-1 Reverse Transcriptase Reveals Key Interactions and a Novel Mechanism of RNase H Inactivation. J Mol Biol 2023; 435:168219. [PMID: 37536391 DOI: 10.1016/j.jmb.2023.168219] [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: 05/05/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
Coupled with PCR, reverse transcriptases (RTs) have been widely used for RNA detection and gene expression analysis. Increased thermostability and nucleic acid binding affinity are desirable RT properties to improve yields and sensitivity of these applications. The effects of amino acid substitutions in the RT RNase H domain were tested in an engineered HIV-1 group O RT, containing mutations K358R/A359G/S360A and devoid of RNase H activity due to the presence of E478Q (O3MQ RT). Twenty mutant RTs with Lys or Arg at positions interacting with the template-primer (i.e., at positions 473-477, 499-502 and 505) were obtained and characterized. Most of them produced significant amounts of cDNA at 37, 50 and 65 °C, as determined in RT-PCR reactions. However, a big loss of activity was observed with mutants A477K/R, S499K/R, V502K/R and Y505K/R, particularly at 65 °C. Binding affinity experiments confirmed that residues 477, 502 and 505 were less tolerant to mutations. Amino acid substitutions Q500K and Q500R produced a slight increase of cDNA synthesis efficiency at 50 and 65 °C, without altering the KD for model DNA/DNA and RNA/DNA heteroduplexes. Interestingly, molecular dynamics simulations predicted that those mutations inactivate the RNase H activity by altering the geometry of the catalytic site. Proof of this unexpected effect was obtained after introducing Q500K or Q500R in the wild-type HIV-1BH10 RT and mutant K358R/A359G/S360A RT. Our results reveal a novel mechanism of RNase H inactivation that preserves RT DNA binding and polymerization efficiency without substituting RNase H active site residues.
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Affiliation(s)
- Javier Martínez Del Río
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, Madrid, Spain
| | - Nerea López-Carrobles
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, Madrid, Spain
| | | | - Óscar Herrera-Chacón
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, Madrid, Spain
| | - Adrián Sánchez-Ibáñez
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, Madrid, Spain
| | - Jesús Mendieta
- Department of Biotechnology, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Madrid, Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, Madrid, Spain.
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Vassilieff H, Geering ADW, Choisne N, Teycheney PY, Maumus F. Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes. Biomolecules 2023; 13:1069. [PMID: 37509105 PMCID: PMC10377300 DOI: 10.3390/biom13071069] [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: 05/31/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The Caulimoviridae is a family of double-stranded DNA viruses that infect plants. The genomes of most vascular plants contain endogenous caulimovirids (ECVs), a class of repetitive DNA elements that is abundant in some plant genomes, resulting from the integration of viral DNA in the chromosomes of germline cells during episodes of infection that have sometimes occurred millions of years ago. In this review, we reflect on 25 years of research on ECVs that has shown that members of the Caulimoviridae have occupied an unprecedented range of ecological niches over time and shed light on their diversity and macroevolution. We highlight gaps in knowledge and prospects of future research fueled by increased access to plant genome sequence data and new tools for genome annotation for addressing the extent, impact, and role of ECVs on plant biology and the origin and evolutionary trajectories of the Caulimoviridae.
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Affiliation(s)
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre de La Réunion, France
- UMR PVBMT, Université de la Réunion, F-97410 Saint-Pierre de La Réunion, France
| | - Florian Maumus
- INRAE, URGI, Université Paris-Saclay, 78026 Versailles, France
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Jin Y, Wang S, Xu S, Zhao S, Xu X, Poongavanam V, Menéndez-Arias L, Zhan P, Liu X. Targeting hepatitis B virus cccDNA levels: recent progress in seeking small molecule drug candidates. Drug Discov Today 2023; 28:103617. [PMID: 37196762 DOI: 10.1016/j.drudis.2023.103617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Hepatitis B virus (HBV) infection is a major global health problem that puts people at high risk of death from cirrhosis and liver cancer. The presence of covalently closed circular DNA (cccDNA) in infected cells is considered to be the main obstacle to curing chronic hepatitis B. At present, the cccDNA cannot be completely eliminated by standard treatments. There is an urgent need to develop drugs or therapies that can reduce HBV cccDNA levels in infected cells. We summarize the discovery and optimization of small molecules that target cccDNA synthesis and degradation. These compounds are cccDNA synthesis inhibitors, cccDNA reducers, core protein allosteric modulators, ribonuclease H inhibitors, cccDNA transcriptional modulators, HBx inhibitors and other small molecules that reduce cccDNA levels. Teaser: HBV covalently closed circular DNA (cccDNA) can be stably maintained in infected cells for a prolonged period, and this is the fundamental reason why hepatitis B cannot be completely cured. Here, we review recent progress in the development of small molecules that can reduce cccDNA levels in infected cells.
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Affiliation(s)
- Yu Jin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shuo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xiangrui Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), 28049 Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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10
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Temereanca A, Ruta S. Strategies to overcome HIV drug resistance-current and future perspectives. Front Microbiol 2023; 14:1133407. [PMID: 36876064 PMCID: PMC9978142 DOI: 10.3389/fmicb.2023.1133407] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
The availability of combined antiretroviral therapy (cART) has revolutionized the course of HIV infection, suppressing HIV viremia, restoring the immune system, and improving the quality of life of HIV infected patients. However, the emergence of drug resistant and multidrug resistant strains remains an important contributor to cART failure, associated with a higher risk of HIV-disease progression and mortality. According to the latest WHO HIV Drug Resistance Report, the prevalence of acquired and transmitted HIV drug resistance in ART naive individuals has exponentially increased in the recent years, being an important obstacle in ending HIV-1 epidemic as a public health threat by 2030. The prevalence of three and four-class resistance is estimated to range from 5 to 10% in Europe and less than 3% in North America. The new drug development strategies are focused on improved safety and resistance profile within the existing antiretroviral classes, discovery of drugs with novel mechanisms of action (e.g., attachment/post-attachment inhibitors, capsid inhibitors, maturation inhibitors, nucleoside reverse transcriptase translocation inhibitors), combination therapies with improved adherence, and treatment simplification with infrequent dosing. This review highlight the current progress in the management of salvage therapy for patients with multidrug-resistant HIV-1 infection, discussing the recently approved and under development antiretroviral agents, as well as the new drug targets that are providing a new avenue for the development of therapeutic interventions in HIV infection.
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Affiliation(s)
- Aura Temereanca
- Virology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Viral Emerging Diseases Department, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Simona Ruta
- Virology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Viral Emerging Diseases Department, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
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11
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Current medicinal chemistry strategies in the discovery of novel HIV-1 ribonuclease H inhibitors. Eur J Med Chem 2022; 243:114760. [PMID: 36152387 DOI: 10.1016/j.ejmech.2022.114760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022]
Abstract
During HIV-1 genome replication, the viral reverse transcriptase-associated ribonuclease H (RT-associated RNase H) activity hydrolyzes the RNA strand of RNA/DNA heteroduplex intermediates. As of today, HIV-1 RNase H inhibitors (RHIs) remain at an investigational level, although none of them reached clinical trials. Therefore, RNase H remains as an attractive target for drug design and development. In this paper, we review the current status of medicinal chemistry strategies aimed at the discovery of novel RHIs, while discussing problems encountered in their characterization and further development, thereby providing an update on recent progress in the field.
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12
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Maslinska M, Kostyra-Grabczak K. The role of virus infections in Sjögren’s syndrome. Front Immunol 2022; 13:823659. [PMID: 36148238 PMCID: PMC9488556 DOI: 10.3389/fimmu.2022.823659] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 08/09/2022] [Indexed: 11/26/2022] Open
Abstract
Primary Sjögren’s syndrome (pSS) is an autoimmune disease with a clinical picture of not only mainly exocrine gland involvement, with dryness symptoms, but also internal organ and systems involvement. The epithelial damage and releasing of antigens, which, in some circumstances, become autoantigens, underlay the pathogenesis of pSS. The activation of autoimmune processes in pSS leads to the hyperactivation of B cells with autoantibody production and other immunological phenomena such as hypergammaglobulinemia, production of cryoglobulins, or formation of extra-nodal lymphoid tissue. Among the risk factors for the development of this disease are viral infections, which themselves can activate autoimmune reactions and influence the host’s immune response. It is known that viruses, through various mechanisms, can influence the immune system and initiate autoimmune reactions. These mechanisms include molecular mimicry, bystander activation, production of superantigens—proteins encoded by viruses—or a programming to produce viral cytokines similar to host cytokines such as, e.g., interleukin-10. Of particular importance for pSS are viruses which not only, as expected, activate the interferon pathway but also play a particular role, directly or indirectly, in B cell activation or present tropism to organs also targeted in the course of pSS. This article is an attempt to present the current knowledge of the influence specific viruses have on the development and course of pSS.
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13
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Zhang L, Wei F, Borrego D, Zhao F, Río JMD, Frutos-Beltrán E, Zhang J, Xu S, López-Carrobles N, Gao S, Kang D, Pannecouque C, Clercq ED, Liu X, Menéndez-Arias L, Zhan P. Design, synthesis, and biological evaluation of novel double-winged galloyl derivatives as HIV-1 RNase H inhibitors. Eur J Med Chem 2022; 240:114563. [DOI: 10.1016/j.ejmech.2022.114563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 01/18/2023]
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14
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Complete genome sequence of pueraria virus A, a new member of the genus Caulimovirus. Arch Virol 2022; 167:1481-1485. [PMID: 35451686 DOI: 10.1007/s00705-022-05431-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/22/2022] [Indexed: 11/02/2022]
Abstract
The complete genome sequence of a new caulimovirus in Pueraria montana was determined using high-throughput sequencing. The 7,572 nucleotide genome of pueraria virus A (PVA) contains genes that encode a movement protein, an aphid transmission factor, a virion-associated protein, a coat protein, a protease + reverse transcriptase + ribonuclease H, and a transactivator/viroplasmin protein, as well as two intergenic regions, which are all common features of members of the genus Caulimovirus. A sequence alignment revealed that the complete genome of PVA shares 66.82% nucleotide sequence identity with strawberry vein banding virus (GenBank accession no. KX249738.1). The results of phylogenetic analysis and the observation that the nucleotide sequence of the polymerase coding region differed by more than 20% indicated that PVA is a member of a new species the genus Caulimovirus, family Caulimoviridae.
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15
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Hadj Hassine I, Ben M’hadheb M, Menéndez-Arias L. Lethal Mutagenesis of RNA Viruses and Approved Drugs with Antiviral Mutagenic Activity. Viruses 2022; 14:841. [PMID: 35458571 PMCID: PMC9024455 DOI: 10.3390/v14040841] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/11/2022] Open
Abstract
In RNA viruses, a small increase in their mutation rates can be sufficient to exceed their threshold of viability. Lethal mutagenesis is a therapeutic strategy based on the use of mutagens, driving viral populations to extinction. Extinction catastrophe can be experimentally induced by promutagenic nucleosides in cell culture models. The loss of HIV infectivity has been observed after passage in 5-hydroxydeoxycytidine or 5,6-dihydro-5-aza-2'-deoxycytidine while producing a two-fold increase in the viral mutation frequency. Among approved nucleoside analogs, experiments with polioviruses and other RNA viruses suggested that ribavirin can be mutagenic, although its mechanism of action is not clear. Favipiravir and molnupiravir exert an antiviral effect through lethal mutagenesis. Both drugs are broad-spectrum antiviral agents active against RNA viruses. Favipiravir incorporates into viral RNA, affecting the G→A and C→U transition rates. Molnupiravir (a prodrug of β-d-N4-hydroxycytidine) has been recently approved for the treatment of SARS-CoV-2 infection. Its triphosphate derivative can be incorporated into viral RNA and extended by the coronavirus RNA polymerase. Incorrect base pairing and inefficient extension by the polymerase promote mutagenesis by increasing the G→A and C→U transition frequencies. Despite having remarkable antiviral action and resilience to drug resistance, carcinogenic risks and genotoxicity are important concerns limiting their extended use in antiviral therapy.
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Affiliation(s)
- Ikbel Hadj Hassine
- Unité de Recherche UR17ES30 “Génomique, Biotechnologie et Stratégies Antivirales”, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir 5000, Tunisia; (I.H.H.); (M.B.M.)
| | - Manel Ben M’hadheb
- Unité de Recherche UR17ES30 “Génomique, Biotechnologie et Stratégies Antivirales”, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir 5000, Tunisia; (I.H.H.); (M.B.M.)
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), 28049 Madrid, Spain
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16
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Dyudeeva ES, Pyshnaya IA. Phosphoryl guanidine oligonucleotides as primers for RNA-dependent DNA synthesis using murine leukemia virus reverse transcriptase. Vavilovskii Zhurnal Genet Selektsii 2022; 26:5-13. [PMID: 35342851 PMCID: PMC8892174 DOI: 10.18699/vjgb-22-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
Modern approaches to the detection and analysis of low-copy-number RNAs are often based on the use of RNA-dependent DNA polymerases, for example, in reverse-transcription PCR. The accuracy and eff iciency of cDNA synthesis in the reverse-transcription reaction catalyzed by reverse transcriptase (RNA-dependent DNA polymerase) signif icantly affect the correctness of the results of PCR diagnostic assays and/or RNA sequencing. In this regard, many studies are focused on the optimization of the reverse-transcription reaction, including the search for more perfect primers necessary to obtain a full-length DNA copy of RNA under study. The best-known completely uncharged analogs of oligonucleotides – morpholine oligonucleotides and peptide nucleic acids – cannot be substrates for enzymes that process nucleic acids. The aim of this work was to conduct a pilot study of uncharged phosphoryl guanidine oligodeoxyribonucleotides (PGOs) as primers for mouse leukemia virus reverse transcriptase (MMLV H-). Specif ic features of elongation of partially and completely uncharged PGO primers were investigated. It was demonstrated that PGOs can be elongated eff iciently, e. g., in the presence of a fragment of human ribosomal RNA having complex spatial structure. It was shown that the proportion (%) of abortive elongation products of a PGO primer depends on buffer ionic strength, nucleotide sequence of the primer, and the presence and location of phosphoryl guanidine groups in the primer. The results indicate the
suitability of PGOs, including completely electroneutral ones, as primers for reverse-transcription PCR, thereby
opening up new prospects for the creation of experimental models for the analysis of highly structured RNA.
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Affiliation(s)
- E. S. Dyudeeva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - I. A. Pyshnaya
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
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17
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Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E. Structural basis of HIV inhibition by L-nucleosides: opportunities for drug development and repurposing. Drug Discov Today 2022; 27:1832-1846. [PMID: 35218925 DOI: 10.1016/j.drudis.2022.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/15/2022] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
Infection with HIV can cripple the immune system and lead to AIDS. Hepatitis B virus (HBV) is a hepadnavirus that causes human liver diseases. Both pathogens are major public health problems affecting millions of people worldwide. The polymerases from both viruses are the most common drug target for viral inhibition, sharing common architecture at their active sites. The L-nucleoside drugs emtricitabine and lamivudine are widely used HIV reverse transcriptase (RT) and HBV polymerase (Pol) inhibitors. Nevertheless, structural details of their binding to RT(Pol)/nucleic acid remained unknown until recently. Here, we discuss the implications of these structures, alongside related complexes with L-dNTPs, for the development of novel L-nucleos(t)ide drugs, and prospects for repurposing them.
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Affiliation(s)
- Francesc X Ruiz
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Anthony Hoang
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher R Dilmore
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA
| | - Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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18
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Martín-Alonso S, Kang D, Martínez Del Río J, Luczkowiak J, Frutos-Beltrán E, Zhang L, Cheng X, Liu X, Zhan P, Menéndez-Arias L. Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase. J Mol Biol 2022; 434:167507. [PMID: 35217069 DOI: 10.1016/j.jmb.2022.167507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
In retroviruses, strand displacement DNA-dependent DNA polymerization catalyzed by the viral reverse transcriptase (RT) is required to synthesize double-stranded proviral DNA. In addition, strand displacement during RNA-dependent DNA synthesis is critical to generate high-quality cDNA for use in molecular biology and biotechnology. In this work, we show that the loss of RNase H activity due to inactivating mutations in HIV-1 RT (e.g. D443N or E478Q) has no significant effect on strand displacement while copying DNA templates, but has a large impact on DNA polymerization in reactions carried out with RNA templates. Similar effects were observed with β-thujaplicinol and other RNase H active site inhibitors, including compounds with dual activity (i.e., characterized also as inhibitors of HIV-1 integrase and/or the RT DNA polymerase). Among them, dual inhibitors of HIV-1 RT DNA polymerase/RNase H activities, containing a 7-hydroxy-6-nitro-2H-chromen-2-one pharmacophore were found to be very potent and effective strand displacement inhibitors in RNA-dependent DNA polymerization reactions. These findings might be helpful in the development of transcriptomics technologies to obtain more uniform read coverages when copying long RNAs and for the construction of more representative libraries avoiding biases towards 5' and 3' ends, while providing valuable information for the development of novel antiretroviral agents.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Javier Martínez Del Río
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Joanna Luczkowiak
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Lina Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Xiqiang Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China.
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain.
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19
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Pimentel SC, Upton HE, Collins K. Separable structural requirements for cDNA synthesis, nontemplated extension, and template jumping by a non-LTR retroelement reverse transcriptase. J Biol Chem 2022; 298:101624. [PMID: 35065960 PMCID: PMC8857657 DOI: 10.1016/j.jbc.2022.101624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Broad evolutionary expansion of polymerase families has enabled specialization of their activities for distinct cellular roles. In addition to template-complementary synthesis, many polymerases extend their duplex products by nontemplated nucleotide addition (NTA). This activity is exploited for laboratory strategies of cloning and sequencing nucleic acids and could have important biological function, although the latter has been challenging to test without separation-of-function mutations. Several retroelement and retroviral reverse transcriptases (RTs) support NTA and also template jumping, by which the RT performs continuous complementary DNA (cDNA) synthesis using physically separate templates. Previous studies that aimed to dissect the relationship between NTA and template jumping leave open questions about structural requirements for each activity and their interdependence. Here, we characterize the structural requirements for cDNA synthesis, NTA, template jumping, and the unique terminal transferase activity of Bombyx mori R2 non-long terminal repeat retroelement RT. With sequence alignments and structure modeling to guide mutagenesis, we generated enzyme variants across motifs generally conserved or specific to RT subgroups. Enzyme variants had diverse NTA profiles not correlated with other changes in cDNA synthesis activity or template jumping. Using these enzyme variants and panels of activity assay conditions, we show that template jumping requires NTA. However, template jumping by NTA-deficient enzymes can be rescued using primer duplex with a specific length of 3′ overhang. Our findings clarify the relationship between NTA and template jumping as well as additional activities of non-long terminal repeat RTs, with implications for the specialization of RT biological functions and laboratory applications.
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Affiliation(s)
- Sydney C Pimentel
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA.
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20
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Boyer PL, Rehm CA, Sneller MC, Mican J, Caplan MR, Dewar R, Ferris AL, Clark P, Johnson A, Maldarelli F, Hughes SH. A Combination of Amino Acid Mutations Leads to Resistance to Multiple Nucleoside Analogs in Reverse Transcriptases from HIV-1 Subtypes B and C. Antimicrob Agents Chemother 2022; 66:e0150021. [PMID: 34723625 PMCID: PMC8765311 DOI: 10.1128/aac.01500-21] [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: 08/02/2021] [Accepted: 10/28/2021] [Indexed: 11/20/2022] Open
Abstract
Resistance to anti-HIV drugs has been a problem from the beginning of antiviral drug treatments. The recent expansion of combination antiretroviral therapy worldwide has led to an increase in resistance to antiretrovirals; understanding the mechanisms of resistance is increasingly important. In this study, we analyzed reverse transcriptase (RT) variants based on sequences derived from an individual who had low-level rebound viremia while undergoing therapy with abacavir, azidothymidine (AZT) (zidovudine), and (-)-l-2',3'-dideoxy-3'-thiacytidine (3TC) (lamivudine). The RT had mutations at positions 64, 67, 70, 184, and 219 and a threonine insertion after amino acid 69 in RT. The virus remained partially susceptible to the nucleoside RT inhibitor (NRTI) regimen. We show how these mutations affect the ability of NRTIs to inhibit DNA synthesis by RT. The presence of the inserted threonine reduced the susceptibility of the RT mutant to inhibition by tenofovir.
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Affiliation(s)
- Paul L. Boyer
- Retroviral Replication Laboratory, National Cancer Institute, Frederick, Maryland, USA
| | - Catherine A. Rehm
- Clinical Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Michael C. Sneller
- Clinical and Molecular Retrovirology Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - JoAnn Mican
- Clinical Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Margaret R. Caplan
- Division of Infectious Disease, Department of Medicine, Harbor-UCLA Medical Center, Los Angeles, California, USA
| | - Robin Dewar
- Division of Infectious Disease, Department of Medicine, Harbor-UCLA Medical Center, Los Angeles, California, USA
| | - Andrea L. Ferris
- Retroviral Replication Laboratory, National Cancer Institute, Frederick, Maryland, USA
| | - Patrick Clark
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Adam Johnson
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Frank Maldarelli
- Clinical Retrovirology Section, National Cancer Institute, Frederick, Maryland, USA
| | - Stephen H. Hughes
- Retroviral Replication Laboratory, National Cancer Institute, Frederick, Maryland, USA
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21
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DARTS: An Algorithm for Domain-Associated Retrotransposon Search in Genome Assemblies. Genes (Basel) 2021; 13:genes13010009. [PMID: 35052350 PMCID: PMC8775202 DOI: 10.3390/genes13010009] [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: 11/30/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 01/08/2023] Open
Abstract
Retrotransposons comprise a substantial fraction of eukaryotic genomes, reaching the highest proportions in plants. Therefore, identification and annotation of retrotransposons is an important task in studying the regulation and evolution of plant genomes. The majority of computational tools for mining transposable elements (TEs) are designed for subsequent genome repeat masking, often leaving aside the element lineage classification and its protein domain composition. Additionally, studies focused on the diversity and evolution of a particular group of retrotransposons often require substantial customization efforts from researchers to adapt existing software to their needs. Here, we developed a computational pipeline to mine sequences of protein-coding retrotransposons based on the sequences of their conserved protein domains—DARTS (Domain-Associated Retrotransposon Search). Using the most abundant group of TEs in plants—long terminal repeat (LTR) retrotransposons (LTR-RTs)—we show that DARTS has radically higher sensitivity for LTR-RT identification compared to the widely accepted tool LTRharvest. DARTS can be easily customized for specific user needs. As a result, DARTS returns a set of structurally annotated nucleotide and amino acid sequences which can be readily used in subsequent comparative and phylogenetic analyses. DARTS may facilitate researchers interested in the discovery and detailed analysis of the diversity and evolution of retrotransposons, LTR-RTs, and other protein-coding TEs.
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22
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Ilina TV, Brosenitsch T, Sluis-Cremer N, Ishima R. Retroviral RNase H: Structure, mechanism, and inhibition. Enzymes 2021; 50:227-247. [PMID: 34861939 DOI: 10.1016/bs.enz.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
All retroviruses encode the enzyme, reverse transcriptase (RT), which is involved in the conversion of the single-stranded viral RNA genome into double-stranded DNA. RT is a multifunctional enzyme and exhibits DNA polymerase and ribonuclease H (RNH) activities, both of which are essential to the reverse-transcription process. Despite the successful development of polymerase-targeting antiviral drugs over the last three decades, no bona fide inhibitor against the RNH activity of HIV-1 RT has progressed to clinical evaluation. In this review article, we describe the retroviral RNH function and inhibition, with primary consideration of the structural aspects of inhibition.
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Affiliation(s)
- Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Teresa Brosenitsch
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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23
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Sluis-Cremer N. Retroviral reverse transcriptase: Structure, function and inhibition. Enzymes 2021; 50:179-194. [PMID: 34861936 DOI: 10.1016/bs.enz.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme that has RNA- and DNA-dependent DNA polymerase activity and ribonuclease H (RNase H) activity, and is responsible for the reverse transcription of retroviral single-stranded RNA into double-stranded DNA. The essential role that RT plays in the human immunodeficiency virus (HIV) life cycle is highlighted by the fact that multiple antiviral drugs-which can be classified into two distinct therapeutic classes-are routinely used to treat and/or prevent HIV infection. This book chapter provides detailed insights into the three-dimensional structure of HIV RT, the biochemical mechanisms of DNA polymerization and RNase H activity, and the mechanisms by which nucleoside/nucleotide and nonnucleoside RT inhibitors block reverse transcription.
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Affiliation(s)
- Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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24
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Abstract
Hepatitis B virus (HBV) is a hepatotropic, partially double-stranded DNA virus that replicates by reverse transcription and is a major cause of chronic liver disease and hepatocellular carcinoma. Reverse transcription is catalyzed by the four-domain multifunctional HBV polymerase (P) protein that has protein-priming, RNA- and DNA-dependent DNA synthesis (i.e., reverse transcriptase), and ribonuclease H activities. P also likely promotes the three strand transfers that occur during reverse transcription, and it may participate in immune evasion by HBV. Reverse transcription is primed by a tyrosine residue in the amino-terminal domain of P, and P remains covalently attached to the product DNA throughout reverse transcription. The reverse transcriptase activity of P is the target for the nucleos(t)ide analog drugs that dominate HBV treatment, and P is the target of ongoing efforts to develop new drugs against both the reverse transcriptase and ribonuclease H activities. Despite the unusual reverse transcription pathway catalyzed by P and the importance of P to HBV therapy, understanding the enzymology and structure of HBV P severely lags that of the retroviral reverse transcriptases due to substantial technical challenges to studying the enzyme. Obtaining a better understanding of P will broaden our appreciation of the diversity among reverse transcribing elements in nature, and will help improve treatment for people chronically infected with HBV.
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Affiliation(s)
- Daniel N Clark
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Razia Tajwar
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States
| | - Jianming Hu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States.
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25
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Menéndez-Arias L, Delgado R. Update and latest advances in antiretroviral therapy. Trends Pharmacol Sci 2021; 43:16-29. [PMID: 34742581 DOI: 10.1016/j.tips.2021.10.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/27/2022]
Abstract
Since the first cases of AIDS appeared in 1981, human immunodeficiency virus type 1 (HIV-1) infection has reached pandemic proportions. Forty years later, research has led to the approval of more than 30 antiretroviral drugs, while combination therapies have turned HIV-1 infection into a chronic, but manageable disease. Still, drug toxicity and acquired and transmitted drug resistance remain as major threats to therapy success. In this review, we provide an overview on currently available anti-HIV drugs and the latest developments in antiretroviral therapy, focused on new antiretroviral agents acting on known and unexploited antiviral targets, prevention therapies aimed to improve available drug combinations, and research on new long-acting therapies, particularly those involving novel drug candidates such as lenacapavir or islatravir.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Rafael Delgado
- Laboratory of Molecular Microbiology. Instituto de Investigación Hospital 12 de Octubre (Imas12) and The University Complutense School of Medicine, Madrid, Spain.
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26
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Khan J, Asoom LIA, Khan M, Chakrabartty I, Dandoti S, Rudrapal M, Zothantluanga JH. Evolution of RNA viruses from SARS to SARS-CoV-2 and diagnostic techniques for COVID-19: a review. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:60. [PMID: 34642633 PMCID: PMC8494164 DOI: 10.1186/s43088-021-00150-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/20/2021] [Indexed: 01/12/2023] Open
Abstract
Background From the start of the twenty-first century up to the year 2021, RNA viruses are the main causative agents of the majority of the disease outbreaks the world has confronted. Recently published reviews on SARS-CoV-2 have mainly focused on its structure, development of the outbreak, relevant precautions, management trials and available therapies. However, in this review, we aim to explore the history, evolution of all coronaviruses and the associated viral outbreaks along with the diagnostics for COVID-19 in the twenty-first century.
Main body We have focused on different RNA viruses’ viz. SARS-CoV, MERS-CoV, and SARS-CoV-2, their classification, and the various disease outbreaks caused by them. In the subsequent section, the comparison of different RNA viruses affecting humans has been made based on the viral genome, structure, time of the outbreak, mode of spread, virulence, causative agents, and transmission. Due to the current mayhem caused by the rapidly emerging virus, special attention is given to SARS-CoV-2, its genome updates, and infectivity. Finally, the current diagnostic techniques such as nucleic acid testing (real time-polymerase chain reaction and loop-mediated isothermal amplification), CRISPR-based diagnostics (CRISPR based DETECTR assay, CRISPR based SHERLOCK test, AIOD-CRISPR, FELUDA, CREST), chest radiographs (computed tomography, X-ray), and serological tests (Lateral flow assay, enzyme-linked immunosorbent assay, chemiluminescent immunoassay, neutralization assay, nano-sensors, blood test, viral sequencing) with their pros and cons, and future diagnostic prospective have been described.
Conclusions The present gloomy scenario mandates clinical manifestations, contact tracing, and laboratory tests as important parameters that need to be taken into consideration to make the final diagnosis.
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Affiliation(s)
- Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952 Saudi Arabia
| | - Lubna Ibrahim Al Asoom
- Physiology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541 Saudi Arabia
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002 India
| | - Ishani Chakrabartty
- Department of Science, P.A. First Grade College (Affiliated To Mangalore University, Mangalore), Nadupadav, Mangalore, Karnataka 574153 India
| | - Sayequa Dandoti
- Department of Biology, Deanship of Preparatory Year, Imam Abdulrahman Bin Faisal University, Dammam, 31541 Saudi Arabia
| | - Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research (Affiliated to Savitribai Phule Pune University, Pune) , Chinchwad, Pune, Maharashtra 411019 India
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam 786004 India
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Pyrroles as Privileged Scaffolds in the Search for New Potential HIV Inhibitors. Pharmaceuticals (Basel) 2021; 14:ph14090893. [PMID: 34577593 PMCID: PMC8468532 DOI: 10.3390/ph14090893] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/04/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV) and remains a global health problem four decades after the report of its first case. Despite success in viral load suppression and the increase in patient survival due to combined antiretroviral therapy (cART), the development of new drugs has become imperative due to strains that have become resistant to antiretrovirals. In this context, there has been a continuous search for new anti-HIV agents based on several chemical scaffolds, including nitrogenated heterocyclic pyrrole rings, which have been included in several compounds with antiretroviral activity. Thus, this review aims to describe pyrrole-based compounds with anti-HIV activity as a new potential treatment against AIDS, covering the period between 2015 and 2020. Our research allowed us to conclude that pyrrole derivatives are still worth exploring, as they may provide highly active compounds targeting different steps of the HIV-1 replication cycle and act with an innovative mechanism.
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28
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Chen XS, Pomerantz RT. DNA Polymerase θ: A Cancer Drug Target with Reverse Transcriptase Activity. Genes (Basel) 2021; 12:1146. [PMID: 34440316 PMCID: PMC8391894 DOI: 10.3390/genes12081146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of precision medicine from the development of Poly (ADP-ribose) polymerase (PARP) inhibitors that preferentially kill cells defective in homologous recombination has sparked wide interest in identifying and characterizing additional DNA repair enzymes that are synthetic lethal with HR factors. DNA polymerase theta (Polθ) is a validated anti-cancer drug target that is synthetic lethal with HR factors and other DNA repair proteins and confers cellular resistance to various genotoxic cancer therapies. Since its initial characterization as a helicase-polymerase fusion protein in 2003, many exciting and unexpected activities of Polθ in microhomology-mediated end-joining (MMEJ) and translesion synthesis (TLS) have been discovered. Here, we provide a short review of Polθ's DNA repair activities and its potential as a drug target and highlight a recent report that reveals Polθ as a naturally occurring reverse transcriptase (RT) in mammalian cells.
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Affiliation(s)
- Xiaojiang S. Chen
- Molecular and Computational Biology, USC Dornsife Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Richard T. Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Menéndez-Arias L, Martín-Alonso S, Frutos-Beltrán E. An Update on Antiretroviral Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:31-61. [PMID: 34258736 DOI: 10.1007/978-981-16-0267-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus (HIV) infection and acquired immune deficiency syndrome (AIDS) still claim many lives across the world. However, research efforts during the last 40 years have led to the approval of over 30 antiretroviral drugs and the introduction of combination therapies that have turned HIV infection into a chronic but manageable disease. In this chapter, we provide an update on current available drugs and treatments, as well as future prospects towards reducing pill burden and developing long-acting drugs and novel antiretroviral therapies. In addition, we summarize efforts to cure HIV, including pharmaceutical strategies focused on the elimination of the virus.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.
| | - Samara Martín-Alonso
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
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30
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Yedavalli VRK, Patil A, Parrish J, Kozak CA. A novel class III endogenous retrovirus with a class I envelope gene in African frogs with an intact genome and developmentally regulated transcripts in Xenopus tropicalis. Retrovirology 2021; 18:20. [PMID: 34261506 PMCID: PMC8278194 DOI: 10.1186/s12977-021-00564-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/29/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Retroviruses exist as exogenous infectious agents and as endogenous retroviruses (ERVs) integrated into host chromosomes. Such endogenous retroviruses (ERVs) are grouped into three classes roughly corresponding to the seven genera of infectious retroviruses: class I (gamma-, epsilonretroviruses), class II (alpha-, beta-, delta-, lentiretroviruses) and class III (spumaretroviruses). Some ERVs have counterparts among the known infectious retroviruses, while others represent paleovirological relics of extinct or undiscovered retroviruses. RESULTS Here we identify an intact ERV in the Anuran amphibian, Xenopus tropicalis. XtERV-S has open reading frames (ORFs) for gag, pol (polymerase) and env (envelope) genes, with a small additional ORF in pol and a serine tRNA primer binding site. It has unusual features and domain relationships to known retroviruses. Analyses based on phylogeny and functional motifs establish that XtERV-S gag and pol genes are related to the ancient env-less class III ERV-L family but the surface subunit of env is unrelated to known retroviruses while its transmembrane subunit is class I-like. LTR constructs show transcriptional activity, and XtERV-S transcripts are detected in embryos after the maternal to zygotic mid-blastula transition and before the late tailbud stage. Tagged Gag protein shows typical subcellular localization. The presence of ORFs in all three protein-coding regions along with identical 5' and 3' LTRs (long terminal repeats) indicate this is a very recent germline acquisition. There are older, full-length, nonorthologous, defective copies in Xenopus laevis and the distantly related African bullfrog, Pyxicephalus adspersus. Additional older, internally deleted copies in X. tropicalis carry a 300 bp LTR substitution. CONCLUSIONS XtERV-S represents a genera-spanning member of the largely env-less class III ERV that has ancient and modern copies in Anurans. This provirus has an env ORF with a surface subunit unrelated to known retroviruses and a transmembrane subunit related to class I gammaretroviruses in sequence and organization, and is expressed in early embryogenesis. Additional XtERV-S-related but defective copies are present in X. tropicalis and other African frog taxa. XtERV-S is an unusual class III ERV variant, and it may represent an important transitional retroviral form that has been spreading in African frogs for tens of millions of years.
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Affiliation(s)
- Venkat R K Yedavalli
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Akash Patil
- Department of Biomedical Engineering, John Hopkins University, Baltimore, MD, 21205, USA
| | - Janay Parrish
- Internal Medicine, Northwell Health, Lenox Hill Hospital, New York, NY, 10075, USA
| | - Christine A Kozak
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA.
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Shrivastava N, Husain A, Rashid M, Alsabeelah NF, Karim S, Siddiqui NA. Recent Advances Towards Treatment of HIV: Synthesis and SAR Studies. Mini Rev Med Chem 2021; 21:471-499. [PMID: 30864523 DOI: 10.2174/1389557519666190312170158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/03/2019] [Accepted: 03/06/2019] [Indexed: 11/22/2022]
Abstract
In the present study, authors want to encourage the research exertions through structureactivity relationship for the identification of effective molecules for the treatment of Human immunodeficiency virus because nowadays AIDS is considered as one of the main causes of death in human beings. A diversity of biological resources has been searched and developed for the treatment of HIV but unfortunately, until now, no medicine is found to be fully effective and safe for the cure of patients. Human immunodeficiency virus is a type of lentivirus which causes the infection of HIV and once it enters the human body, it stays for a longer period of time triggering immunodeficiency syndrome. For searching and developing new potent and effective anti-HIV molecules, medicinal chemists have engaged in countless targets with the structure-activity relationship (SAR) of molecules and on this basis, many antiretroviral therapies have been developed to cure HIV infection. Most of these new searched molecules have been found to be clinically active against various types of AIDS patient and auxiliary research in this area may lead to better treatment in the near future. This article encompasses and highlights the recent advancement of innumerable inhibitors laterally through synthetic, semi-synthetic and structure-activity relationship approaches.
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Affiliation(s)
- Neelima Shrivastava
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Hamdard University), New Delhi 110062, India
| | - Asif Husain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Hamdard University), New Delhi 110062, India
| | - Mohammad Rashid
- College of Pharmacy and Dentistry, Buraydah Colleges, Buraydah, Al-Qassim 31717, Saudi Arabia
| | - Nimer Fehaid Alsabeelah
- College of Pharmacy and Dentistry, Buraydah Colleges, Buraydah, Al-Qassim 31717, Saudi Arabia
| | - Shahid Karim
- Department of Pharmacology, College of Medicine, King Abdul Aziz University, Jeddah 21589, Saudi Arabia
| | - Nasir Ali Siddiqui
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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Chandramouly G, Zhao J, McDevitt S, Rusanov T, Hoang T, Borisonnik N, Treddinick T, Lopezcolorado FW, Kent T, Siddique LA, Mallon J, Huhn J, Shoda Z, Kashkina E, Brambati A, Stark JM, Chen XS, Pomerantz RT. Polθ reverse transcribes RNA and promotes RNA-templated DNA repair. SCIENCE ADVANCES 2021; 7:7/24/eabf1771. [PMID: 34117057 PMCID: PMC8195485 DOI: 10.1126/sciadv.abf1771] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/23/2021] [Indexed: 05/12/2023]
Abstract
Genome-embedded ribonucleotides arrest replicative DNA polymerases (Pols) and cause DNA breaks. Whether mammalian DNA repair Pols efficiently use template ribonucleotides and promote RNA-templated DNA repair synthesis remains unknown. We find that human Polθ reverse transcribes RNA, similar to retroviral reverse transcriptases (RTs). Polθ exhibits a significantly higher velocity and fidelity of deoxyribonucleotide incorporation on RNA versus DNA. The 3.2-Å crystal structure of Polθ on a DNA/RNA primer-template with bound deoxyribonucleotide reveals that the enzyme undergoes a major structural transformation within the thumb subdomain to accommodate A-form DNA/RNA and forms multiple hydrogen bonds with template ribose 2'-hydroxyl groups like retroviral RTs. Last, we find that Polθ promotes RNA-templated DNA repair in mammalian cells. These findings suggest that Polθ was selected to accommodate template ribonucleotides during DNA repair.
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Affiliation(s)
- Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jiemin Zhao
- Molecular and Computational Biology, USC Dornsife Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Shane McDevitt
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Timur Rusanov
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Trung Hoang
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nikita Borisonnik
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Taylor Treddinick
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Tatiana Kent
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Labiba A Siddique
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Joseph Mallon
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jacklyn Huhn
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zainab Shoda
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ekaterina Kashkina
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alessandra Brambati
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Jeremy M Stark
- Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology, USC Dornsife Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Richard T Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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Bandyopadhyay S, Douglass J, Kapell S, Khan N, Feitosa-Suntheimer F, Klein JA, Temple J, Brown-Culbertson J, Tavares AH, Saeed M, Lau NC. DNA templates with blocked long 3' end single-stranded overhangs (BL3SSO) promote bona fide Cas9-stimulated homology-directed repair of long transgenes into endogenous gene loci. G3-GENES GENOMES GENETICS 2021; 11:6275753. [PMID: 33989385 PMCID: PMC8496256 DOI: 10.1093/g3journal/jkab169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022]
Abstract
Knock-in of large transgenes by Cas9-mediated homology-directed repair (HDR) is an extremely inefficient process. Although the use of single-stranded oligonucleotides (ssODN) as an HDR donor has improved the integration of smaller transgenes, they do not support efficient insertion of large DNA sequences. In an effort to gain insights into the mechanism(s) governing the HDR-mediated integration of larger transgenes and to improve the technology, we conducted knock-in experiments targeting the human EMX1 locus and applied rigorous genomic PCR analyses in the human HEK293 cell line. This exercise revealed an unexpected molecular complication arising from the transgene HDR being initiated at the single homology arm and the subsequent genomic integration of plasmid backbone sequences. To pivot around this problem, we devised a novel PCR-constructed template containing blocked long 3' single-stranded overhangs (BL3SSO) that greatly improved the efficiency of bona fide Cas9-stimulated HDR at the EMX1 locus. We further refined BL3SSO technology and successfully used it to insert GFP transgenes into two important interferon-stimulated genes (ISGs) loci, Viperin/RSAD2, and ISG15. This study demonstrates the utility of the BL3SSO platform for inserting long DNA sequences into both constitutive and inducible endogenous loci to generate novel human cell lines for the study of important biological processes.
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Affiliation(s)
- Saptaparni Bandyopadhyay
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Joseph Douglass
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Sebastian Kapell
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Nazimuddin Khan
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | | | - Jenny A Klein
- Department of Biology, Brandeis University, Waltham, MA 02453, USA.,Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Jasmine Temple
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Jayce Brown-Culbertson
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Alexander H Tavares
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Nelson C Lau
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA 02118, USA.,National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA.,Genome Science Institute, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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Andrzejewska A, Zawadzka M, Gumna J, Garfinkel DJ, Pachulska-Wieczorek K. In vivo structure of the Ty1 retrotransposon RNA genome. Nucleic Acids Res 2021; 49:2878-2893. [PMID: 33621339 PMCID: PMC7969010 DOI: 10.1093/nar/gkab090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/25/2022] Open
Abstract
Long terminal repeat (LTR)-retrotransposons constitute a significant part of eukaryotic genomes and influence their function and evolution. Like other RNA viruses, LTR-retrotransposons efficiently utilize their RNA genome to interact with host cell machinery during replication. Here, we provide the first genome-wide RNA secondary structure model for a LTR-retrotransposon in living cells. Using SHAPE probing, we explore the secondary structure of the yeast Ty1 retrotransposon RNA genome in its native in vivo state and under defined in vitro conditions. Comparative analyses reveal the strong impact of the cellular environment on folding of Ty1 RNA. In vivo, Ty1 genome RNA is significantly less structured and more dynamic but retains specific well-structured regions harboring functional cis-acting sequences. Ribosomes participate in the unfolding and remodeling of Ty1 RNA, and inhibition of translation initiation stabilizes Ty1 RNA structure. Together, our findings support the dual role of Ty1 genomic RNA as a template for protein synthesis and reverse transcription. This study also contributes to understanding how a complex multifunctional RNA genome folds in vivo, and strengthens the need for studying RNA structure in its natural cellular context.
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Affiliation(s)
- Angelika Andrzejewska
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Małgorzata Zawadzka
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Ma Y, Frutos-Beltrán E, Kang D, Pannecouque C, De Clercq E, Menéndez-Arias L, Liu X, Zhan P. Medicinal chemistry strategies for discovering antivirals effective against drug-resistant viruses. Chem Soc Rev 2021; 50:4514-4540. [PMID: 33595031 DOI: 10.1039/d0cs01084g] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During the last forty years we have witnessed impressive advances in the field of antiviral drug discovery culminating with the introduction of therapies able to stop human immunodeficiency virus (HIV) replication, or cure hepatitis C virus infections in people suffering from liver disease. However, there are important viral diseases without effective treatments, and the emergence of drug resistance threatens the efficacy of successful therapies used today. In this review, we discuss strategies to discover antiviral compounds specifically designed to combat drug resistance. Currently, efforts in this field are focused on targeted proteins (e.g. multi-target drug design strategies), but also on drug conformation (either improving drug positioning in the binding pocket or introducing conformational constraints), in the introduction or exploitation of new binding sites, or in strengthening interaction forces through the introduction of multiple hydrogen bonds, covalent binding, halogen bonds, additional van der Waals forces or multivalent binding. Among the new developments, proteolysis targeting chimeras (PROTACs) have emerged as a valid approach taking advantage of intracellular mechanisms involving protein degradation by the ubiquitin-proteasome system. Finally, several molecules targeting host factors (e.g. human dihydroorotate dehydrogenase and DEAD-box polypeptide 3) have been identified as broad-spectrum antiviral compounds. Implementation of herein described medicinal chemistry strategies are expected to contribute to the discovery of new drugs effective against current and future threats due to emerging and re-emerging viral pandemics.
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Affiliation(s)
- Yue Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, P. R. China.
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Álvarez M, Sapena-Ventura E, Luczkowiak J, Martín-Alonso S, Menéndez-Arias L. Analysis and Molecular Determinants of HIV RNase H Cleavage Specificity at the PPT/U3 Junction. Viruses 2021; 13:v13010131. [PMID: 33477685 PMCID: PMC7831940 DOI: 10.3390/v13010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/05/2021] [Accepted: 01/14/2021] [Indexed: 02/05/2023] Open
Abstract
HIV reverse transcriptases (RTs) convert viral genomic RNA into double-stranded DNA. During reverse transcription, polypurine tracts (PPTs) resilient to RNase H cleavage are used as primers for plus-strand DNA synthesis. Nonnucleoside RT inhibitors (NNRTIs) can interfere with the initiation of plus-strand DNA synthesis by enhancing PPT removal, while HIV RT connection subdomain mutations N348I and N348I/T369I mitigate this effect by altering RNase H cleavage specificity. Now, we demonstrate that among approved nonnucleoside RT inhibitors (NNRTIs), nevirapine and doravirine show the largest effects. The combination N348I/T369I in HIV-1BH10 RT has a dominant effect on the RNase H cleavage specificity at the PPT/U3 site. Biochemical studies showed that wild-type HIV-1 and HIV-2 RTs were able to process efficiently and accurately all tested HIV PPT sequences. However, the cleavage accuracy at the PPT/U3 junction shown by the HIV-2EHO RT was further improved after substituting the sequence YQEPFKNLKT of HIV-1BH10 RT (positions 342–351) for the equivalent residues of the HIV-2 enzyme (HQGDKILKV). Our results highlight the role of β-sheets 17 and 18 and their connecting loop (residues 342–350) in the connection subdomain of the large subunit, in determining the RNase H cleavage window of HIV RTs.
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Mestre MR, González-Delgado A, Gutiérrez-Rus LI, Martínez-Abarca F, Toro N. Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. Nucleic Acids Res 2021; 48:12632-12647. [PMID: 33275130 PMCID: PMC7736814 DOI: 10.1093/nar/gkaa1149] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.
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Affiliation(s)
- Mario Rodríguez Mestre
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Alejandro González-Delgado
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Luis I Gutiérrez-Rus
- Departamento de Química Física. Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
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Vanangamudi M, Nair PC, Engels SEM, Palaniappan S, Namasivayam V. Structural Insights to Human Immunodeficiency Virus (HIV-1) Targets and Their Inhibition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:63-95. [PMID: 34258737 DOI: 10.1007/978-981-16-0267-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human immunodeficiency virus (HIV) is a deadly virus that attacks the body's immune system, subsequently leading to AIDS (acquired immunodeficiency syndrome) and ultimately death. Currently, there is no vaccine or effective cure for this infection; however, antiretrovirals that act at various phases of the virus life cycle have been useful to control the viral load in patients. One of the major problems with antiretroviral therapies involves drug resistance. The three-dimensional structure from crystallography studies are instrumental in understanding the structural basis of drug binding to various targets. This chapter provides key insights into different targets and drugs used in the treatment from a structural perspective. Specifically, an insight into the binding characteristics of drugs at the active and allosteric sites of different targets and the importance of targeting allosteric sites for design of new-generation antiretrovirals to overcome complex and resistant forms of the virus has been reviewed.
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Affiliation(s)
- Murugesan Vanangamudi
- Department of Pharmaceutical Chemistry, Amity Institute of Pharmacy, Amity University Gwalior, Gwalior, Madhya Pradesh, India
| | - Pramod C Nair
- Department of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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Nucleocapsid Protein Precursors NCp9 and NCp15 Suppress ATP-Mediated Rescue of AZT-Terminated Primers by HIV-1 Reverse Transcriptase. Antimicrob Agents Chemother 2020; 64:AAC.00958-20. [PMID: 32747359 DOI: 10.1128/aac.00958-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/29/2020] [Indexed: 01/20/2023] Open
Abstract
In HIV-1, development of resistance to AZT (3'-azido-3'-deoxythymidine) is mediated by the acquisition of thymidine analogue resistance mutations (TAMs) (i.e., M41L, D67N, K70R, L210W, T215F/Y, and K219E/Q) in the viral reverse transcriptase (RT). Clinically relevant combinations of TAMs, such as M41L/T215Y or D67N/K70R/T215F/K219Q, enhance the ATP-mediated excision of AZT monophosphate (AZTMP) from the 3' end of the primer, allowing DNA synthesis to continue. Additionally, during HIV-1 maturation, the Gag polyprotein is cleaved to release a mature nucleocapsid protein (NCp7) and two intermediate precursors (NCp9 and NCp15). NC proteins interact with the viral genome and facilitate the reverse transcription process. Using wild-type and TAM-containing RTs, we showed that both NCp9 and NCp15 inhibited ATP-mediated rescue of AZTMP-terminated primers annealed to RNA templates but not DNA templates, while NCp7 had no effect on rescue activity. RNase H inactivation by introducing the active-site mutation E478Q led to the loss of the inhibitory effect shown by NCp9. NCp15 had a stimulatory effect on the RT's RNase H activity not observed with NCp7 and NCp9. However, analysis of RNase H cleavage patterns revealed that in the presence of NCp9, RNA/DNA complexes containing duplexes of 12 bp had reduced stability in comparison with those obtained in the absence of NC or with NCp7 or NCp15. These effects are expected to have a strong influence on the inhibitory action of NCp9 and NCp15 by affecting the efficiency of RNA-dependent DNA polymerization after unblocking DNA primers terminated with AZTMP and other nucleotide analogues.
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Abstract
We report here crystal structures of a reverse transcriptase RTX, which was evolved in vitro from the B family polymerase KOD, in complex with either a DNA duplex or an RNA-DNA hybrid. Compared with the apo, binary, and ternary complex structures of the original KOD polymerase, the 16 substitutions that result in the function of copying RNA to DNA do not change the overall protein structure. Only six substitutions occur at the substrate-binding surface, and the others change domain-domain interfaces in the polymerase to enable RNA-DNA hybrid binding and reverse transcription. Most notably, F587L at the Palm and Thumb interface stabilizes the open and apo conformation of the Thumb. The intrinsically flexible Thumb domain seems to play a major role in accommodating the RNA-DNA hybrid product distal to the active site. This is reminiscent of naturally occurring RNA-dependent DNA polymerases, including telomerase, which have a dramatically augmented Thumb domain, and of reverse transcriptase, which extends its Thumb with the RNase H domain.
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Cullen H, Schorn AJ. Endogenous Retroviruses Walk a Fine Line between Priming and Silencing. Viruses 2020; 12:v12080792. [PMID: 32718022 PMCID: PMC7472051 DOI: 10.3390/v12080792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/31/2022] Open
Abstract
Endogenous retroviruses (ERVs) in mammals are closely related to infectious retroviruses and utilize host tRNAs as a primer for reverse transcription and replication, a hallmark of long terminal repeat (LTR) retroelements. Their dependency on tRNA makes these elements vulnerable to targeting by small RNAs derived from the 3′-end of mature tRNAs (3′-tRFs), which are highly expressed during epigenetic reprogramming and potentially protect many tissues in eukaryotes. Here, we review some key functions of ERV reprogramming during mouse and human development and discuss how small RNA-mediated silencing maintains genome stability when ERVs are temporarily released from heterochromatin repression. In particular, we take a closer look at the tRNA primer binding sites (PBS) of two highly active ERV families in mice and their sequence variation that is shaped by the conflict of successful tRNA priming for replication versus evasion of silencing by 3′-tRFs.
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Martín-Alonso S, Frutos-Beltrán E, Menéndez-Arias L. Reverse Transcriptase: From Transcriptomics to Genome Editing. Trends Biotechnol 2020; 39:194-210. [PMID: 32653101 DOI: 10.1016/j.tibtech.2020.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 01/01/2023]
Abstract
Reverse transcriptases (RTs) are enzymes that can generate a complementary strand of DNA (cDNA) from RNA. Coupled with PCR, RTs have been widely used to detect RNAs and to clone expressed genes. Classical retroviral RTs have been improved by protein engineering. These enzymes and newly characterized RTs are key elements in the development of next-generation sequencing techniques that are now being applied to the study of transcriptomics. In addition, engineered RTs fused to a CRISPR/Cas9 nickase have recently shown great potential as tools to manipulate eukaryotic genomes. In this review, we discuss the properties and uses of wild type and engineered RTs in biotechnological applications, from conventional RT-PCR to recently introduced prime editing.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain. @cbm.csic.es
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Sánchez-Murcia PA, de Castro S, García-Aparicio C, Jiménez MA, Corona A, Tramontano E, Sluis-Cremer N, Menéndez-Arias L, Velázquez S, Gago F, Camarasa MJ. Peptides Mimicking the β7/β8 Loop of HIV-1 Reverse Transcriptase p51 as "Hotspot-Targeted" Dimerization Inhibitors. ACS Med Chem Lett 2020; 11:811-817. [PMID: 32435389 DOI: 10.1021/acsmedchemlett.9b00623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/24/2020] [Indexed: 02/04/2023] Open
Abstract
A conformationally constrained short peptide designed to target a protein-protein interaction hotspot in HIV-1 reverse transcriptase (RT) disrupts p66-p51 interactions and paves the way to the development of novel RT dimerization inhibitors.
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Affiliation(s)
| | - Sonia de Castro
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | | | - M. Angeles Jiménez
- Instituto de Química-Física Rocasolano (IQFR, CSIC), Serrano 119, E-28006Madrid, Spain
| | - Angela Corona
- University of Cagliari, Department of Life and Environmental Sciences, Cittadella Universitaria di
Monserrato, 09042 Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- University of Cagliari, Department of Life and Environmental Sciences, Cittadella Universitaria di
Monserrato, 09042 Monserrato, Cagliari, Italy
| | - Nicolas Sluis-Cremer
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, Pennsylvania 15261, United States
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (CBMSO, CSIC & Universidad Autónoma de Madrid), Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Sonsoles Velázquez
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas, Universidad de Alcalá, Unidad Asociada CSIC, E-28805 Alcalá de Henares, Madrid, Spain
| | - María-José Camarasa
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
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Martín-Alonso S, Álvarez M, Nevot M, Martínez MÁ, Menéndez-Arias L. Defective Strand-Displacement DNA Synthesis Due to Accumulation of Thymidine Analogue Resistance Mutations in HIV-2 Reverse Transcriptase. ACS Infect Dis 2020; 6:1140-1153. [PMID: 32129987 DOI: 10.1021/acsinfecdis.9b00512] [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] [Indexed: 12/31/2022]
Abstract
Retroviral reverse transcriptases (RTs) have the ability to carry out strand displacement DNA synthesis in the absence of accessory proteins. Although studies with RTs and other DNA polymerases suggest that fingers subdomain residues participate in strand displacement, molecular determinants of this activity are still unknown. A mutant human immunodeficiency virus type 2 (HIV-2) RT (M41L/D67N/K70R/S215Y) with low strand displacement activity was identified after screening a panel of purified enzymes, including several antiretroviral drug-resistant HIV-1 and HIV-2 RTs. In HIV-1, resistance to zidovudine and other thymidine analogues is conferred by different combinations of M41L, D67N, K70R, L210W, T215F/Y, and K219E/Q (designated as thymidine analogue resistance-associated mutations (TAMs)). However, those changes are rarely selected in HIV-2. We show that the strand displacement activity of HIV-2ROD mutants M41L/S215Y and D67N/K70R was only slightly reduced compared to the wild-type RT. In contrast, mutants D67N/K70R/S215Y and M41L/D67N/K70R/S215Y were the most defective RTs in reactions carried out with nicked and gapped substrates. Moreover, these enzymes showed the lowest nucleotide incorporation rates in assays carried out with strand displacement substrates. Unlike in HIV-2, substitutions M41L/T215Y and D67N/K70R/T215Y/K219Q had no effect on the strand displacement activity of HIV-1BH10 RT. The strand displacement efficiencies of HIV-2ROD RTs were consistent with the lower replication capacity of HIV-2 strains bearing the four major TAMs in their RT. Our results highlight the role of the fingers subdomain in strand displacement. These findings might be important for the development of strand-displacement defective RTs.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biologı́a Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Cientı́ficas and Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Mar Álvarez
- Centro de Biologı́a Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Cientı́ficas and Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - María Nevot
- Laboratori de Retrovirologia, Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, 08916 Barcelona, Spain
| | - Miguel Á. Martínez
- Laboratori de Retrovirologia, Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, 08916 Barcelona, Spain
| | - Luis Menéndez-Arias
- Centro de Biologı́a Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Cientı́ficas and Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
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Tramontano E, Corona A, Menéndez-Arias L. Ribonuclease H, an unexploited target for antiviral intervention against HIV and hepatitis B virus. Antiviral Res 2019; 171:104613. [PMID: 31550450 DOI: 10.1016/j.antiviral.2019.104613] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/18/2022]
Abstract
Ribonucleases H (RNases H) are endonucleolytic enzymes, evolutionarily related to retroviral integrases, DNA transposases, resolvases and numerous nucleases. RNases H cleave RNA in RNA/DNA hybrids and their activity plays an important role in the replication of prokaryotic and eukaryotic genomes, as well as in the replication of reverse-transcribing viruses. During reverse transcription, the RNase H activity of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) degrades the viral genomic RNA to facilitate the synthesis of viral double-stranded DNA. HIV and HBV reverse transcriptases contain DNA polymerase and RNase H domains that act in a coordinated manner to produce double-stranded viral DNA. Although RNase H inhibitors have not been developed into licensed drugs, recent progress has led to the identification of a number of small molecules with inhibitory activity at low micromolar or even nanomolar concentrations. These compounds can be classified into metal-chelating active site inhibitors and allosteric inhibitors. Among them, α-hydroxytropolones, N-hydroxyisoquinolinediones and N-hydroxypyridinediones represent chemotypes active against both HIV and HBV RNases H. In this review we summarize recent developments in the field including the identification of novel RNase H inhibitors, compounds with dual inhibitory activity, broad specificity and efforts to decrease their toxicity.
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Affiliation(s)
- Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
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Zhao JH, Guo HS. Trans-kingdom RNA interactions drive the evolutionary arms race between hosts and pathogens. Curr Opin Genet Dev 2019; 58-59:62-69. [PMID: 31472442 DOI: 10.1016/j.gde.2019.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
Trans-kingdom RNA plays a key role in host-parasite interactions. Hosts export specific endogenous microRNAs (miRNAs) into pathogens to target pathogen virulence genes and inhibit their invasion. In addition, trans-kingdom sRNAs produced by parasites may function as RNA effectors to suppress host immunity. Here, we summarize recent, important findings regarding trans-kingdom RNA and focus on the roles of trans-kingdom RNA in driving an evolutionary arms race between host and pathogen. We suggest that trans-kingdom RNA is a new platform for such arms races. Furthermore, we conjecture that trans-kingdom RNA contributes to horizontal gene transfer (HGT) involved in host-pathogen interactions. In addition, we propose that trans-kingdom RNA exchange and RNA driven HGT can have a great impact on the evolutionary ecology of interacting species.
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Affiliation(s)
- Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, 100049 Beijing, China.
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Rosani U, Bai CM, Maso L, Shapiro M, Abbadi M, Domeneghetti S, Wang CM, Cendron L, MacCarthy T, Venier P. A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks. BMC Evol Biol 2019; 19:149. [PMID: 31337330 PMCID: PMC6651903 DOI: 10.1186/s12862-019-1472-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
Background Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. Results We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. Conclusions We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1472-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 32121, Padova, Italy. .,Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute (AWI), Wadden Sea Station, 25992, List auf Sylt, Germany.
| | - Chang-Ming Bai
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Lorenzo Maso
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Miriam Abbadi
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, Italy
| | | | - Chong-Ming Wang
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Laura Cendron
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Paola Venier
- Department of Biology, University of Padova, 32121, Padova, Italy.
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Hyjek M, Figiel M, Nowotny M. RNases H: Structure and mechanism. DNA Repair (Amst) 2019; 84:102672. [PMID: 31371183 DOI: 10.1016/j.dnarep.2019.102672] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022]
Abstract
RNases H are a family of endonucleases that hydrolyze RNA residues in various nucleic acids. These enzymes are present in all branches of life, and their counterpart domains are also found in reverse transcriptases (RTs) from retroviruses and retroelements. RNases H are divided into two main classes (RNases H1 and H2 or type 1 and type 2 enzymes) with common structural features of the catalytic domain but different range of substrates for enzymatic cleavage. Additionally, a third class is found in some Archaea and bacteria. Besides distinct cellular functions specific for each type of RNases H, this family of proteins is generally involved in the maintenance of genome stability with overlapping and cooperative role in removal of R-loops thus preventing their accumulation. Extensive biochemical and structural studies of RNases H provided not only a comprehensive and complete picture of their mechanism but also revealed key basic principles of nucleic acid recognition and processing. RNase H1 is present in prokaryotes and eukaryotes and cleaves RNA in RNA/DNA hybrids. Its main function is hybrid removal, notably in the context of R-loops. RNase H2, which is also present in all branches of life, can play a similar role but it also has a specialized function in the cleavage of single ribonucleotides embedded in the DNA. RNase H3 is present in Archaea and bacteria and is closely related to RNase H2 in sequence and structure but has RNase H1-like biochemical properties. This review summarizes the mechanisms of substrate recognition and enzymatic cleavage by different classes of RNases H with particular insights into structural features of nucleic acid binding, specificity towards RNA and/or DNA strands and catalysis.
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Affiliation(s)
- Malwina Hyjek
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Marcin Nowotny
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
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Gao P, Cheng X, Sun L, Song S, Álvarez M, Luczkowiak J, Pannecouque C, De Clercq E, Menéndez-Arias L, Zhan P, Liu X. Design, synthesis and biological evaluation of 3-hydroxyquinazoline-2,4(1H,3H)-diones as dual inhibitors of HIV-1 reverse transcriptase-associated RNase H and integrase. Bioorg Med Chem 2019; 27:3836-3845. [PMID: 31324562 DOI: 10.1016/j.bmc.2019.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 11/25/2022]
Abstract
A novel series of 3-hydroxyquinazoline-2,4(1H,3H)-diones derivatives has been designed and synthesized. Their biochemical characterization revealed that most of the compounds were effective inhibitors of HIV-1 RNase H activity at sub to low micromolar concentrations. Among them, II-4 was the most potent in enzymatic assays, showing an IC50 value of 0.41 ± 0.13 μM, almost five times lower than the IC50 obtained with β-thujaplicinol. In addition, II-4 was also effective in inhibiting HIV-1 IN strand transfer activity (IC50 = 0.85 ± 0.18 μM) but less potent than raltegravir (IC50 = 71 ± 14 nM). Despite its relatively low cytotoxicity, the efficiency of II-4 in cell culture was limited by its poor membrane permeability. Nevertheless, structure-activity relationships and molecular modeling studies confirmed the importance of tested 3-hydroxyquinazoline-2,4(1H,3H)-diones as useful leads for further optimization.
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Affiliation(s)
- Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Xiqiang Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Mar Álvarez
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain
| | - Joanna Luczkowiak
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China.
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De Wit F, Pillalamarri SR, Sebastián-Martín A, Venkatesham A, Van Aerschot A, Debyser Z. Design of reverse transcriptase-specific nucleosides to visualize early steps of HIV-1 replication by click labeling. J Biol Chem 2019; 294:11863-11875. [PMID: 31201270 DOI: 10.1074/jbc.ra118.007185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 06/06/2019] [Indexed: 11/06/2022] Open
Abstract
Only a small portion of human immunodeficiency virus type 1 (HIV-1) particles entering the host cell results in productive infection, emphasizing the importance of identifying the functional virus population. Because integration of viral DNA (vDNA) is required for productive infection, efficient vDNA detection is crucial. Here, we use click chemistry to label viruses with integrase coupled to eGFP (HIVIN-eGFP) and visualize vDNA. Because click labeling with 5-ethynyl-2'-deoxyuridine is hampered by intense background staining of the host nucleus, we opted for developing HIV-1 reverse transcriptase (RT)-specific 2'-deoxynucleoside analogs that contain a clickable triple bond. We synthesized seven propargylated 2'-deoxynucleosides and tested them for lack of cytotoxicity and viral replication inhibition, RT-specific primer extension and incorporation kinetics in vitro, and the capacity to stain HIV-1 DNA. The triphosphate of analog A5 was specifically incorporated by HIV-1 RT, but no vDNA staining was detected during infection. Analog A3 was incorporated in vitro by HIV-1 RT and human DNA polymerase γ and did enable specific HIV-1 DNA labeling. Additionally, A3 supported mitochondria-specific DNA labeling, in line with the in vitro findings. After obtaining proof-of-principle of RT-specific DNA labeling reported here, further chemical refinement is necessary to develop even more efficient HIV-1 DNA labels without background staining of the nucleus or mitochondria.
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Affiliation(s)
- Flore De Wit
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Sambasiva Rao Pillalamarri
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Alba Sebastián-Martín
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium.,Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid, 28006 Madrid, Spain
| | - Akkaladevi Venkatesham
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
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