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Maekawa M, Oda T, Hanai R. Biochemical analysis of the replication initiator protein of staphylococcal plasmid pC194. Biochimie 2022; 202:85-93. [PMID: 35988842 DOI: 10.1016/j.biochi.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/07/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022]
Abstract
The staphylococcal plasmid pC194 is replicated through the rolling-circle mechanism. Its replication protein RepA has been proposed to initiate replication by making a bond between Y214 and DNA phosphate via transesterification and to terminate it by hydrolyzing DNA with E210 and carrying out strand transfer. We tested this model by examining the catalytic functions of the protein with purified RepA proteins and single-stranded DNA oligomers. The wild-type RepA formed a covalent bond with the DNA phosphate at the predicted initiation site. It hydrolyzed the phosphodiester bond at the site, which activity was found to depend on the presence of a large pseudopalindrome contained in the replication origin. The protein carried out a strand-transfer reaction which mimicked the termination step of replication. A Y214F and an E210A mutant respectively lacked the transesterification and the hydrolytic activity. These results are consistent with the previously proposed model, which was based solely on molecular genetics results. In addition, an E142A mutant was found to lack both activities, suggesting that the residue may coordinate the divalent cation necessary for them. A possible role of the pseudopalindrome in controlling the two activities of RepA during a replication cycle is also discussed.
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Affiliation(s)
- Michinari Maekawa
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Takashi Oda
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Ryo Hanai
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan.
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Huang YL, Kawai G, Hasegawa A, Kannagi M, Masuda T. Impact of 5'-end nucleotide modifications of HIV-1 genomic RNA on reverse transcription. Biochem Biophys Res Commun 2019; 516:1145-1151. [PMID: 31284953 DOI: 10.1016/j.bbrc.2019.06.152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 11/20/2022]
Abstract
Reverse transcription of retroviral RNA is accomplished through a minus-strand strong stop cDNA (-sscDNA) synthesis and subsequent strand-transfer reactions. We have previously reported a critical role of guanosine (G) number at 5'-terminal of HIV-1 RNA for successful strand-transfer of -sscDNA. In this study, role(s) of the cap consisting of 7-methyl guanosine (7mG), a hallmark of transcripts generated by RNA polymerase II, at the 5'-end G nucleotide (5'-G) of HIV-1 RNA were examined. In parallel, contribution of highly conserved GGG tract located at the U3/R boundary in 3' terminal region of viral RNA (3'-GGG tract) was also addressed. The in vitro reverse transcription analysis using synthetic HIV-1 RNAs possessing the 5'-G with cap or triphosphate form demonstrated that the 5'-cap significantly increased strand-transfer efficiency of -sscDNA. Meanwhile, effect of the 5'-cap on the strand-transfer was retained in the reaction using mutant HIV-1 RNAs in which two Gs were deleted from the 3'-GGG tract. Lack of apparent contribution of the 3'-GGG tract during strand-transfer events in vitro was reproduced in the context of HIV-1 replication within cells. Instead, we noticed that the 3'-GGG tract might be required for efficient gene expression from proviral DNA. These results indicated that 7mG of the cap on HIV-1 RNA might not be reverse-transcribed and a possible role of the 3'-GGG tract to accept the non-template nucleotide addition during -sscDNA synthesis might be less likely. The 5'-G modifications of HIV-1 RNAs by the cap- or phosphate-removal enzyme revealed that the cap or monophosphate form of the 5'-G was preferred for the 1st strand-transfer compared to the triphosphate or non-phosphate form. Taken together, a status of the 5'-G determined strand-transfer efficiency of -sscDNA without affecting the non-template nucleotide addition, probably by affecting association of the 5'-G with 3'-end region of viral RNA.
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Affiliation(s)
- Yu-Lun Huang
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba, 275-0016, Japan
| | - Atsuhiko Hasegawa
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Mari Kannagi
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan
| | - Takao Masuda
- Department of Immunotherapeutics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Yushima, 1-5-45, Bunkyo-ku, Tokyo, 113-8519, Japan.
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Abstract
An infectious retroviral particle contains 1000-1500 molecules of the nucleocapsid protein (NC) that cover the diploid RNA genome. NC is a small zinc finger protein that possesses nucleic acid chaperone activity that enables NC to rearrange DNA and RNA molecules into the most thermodynamically stable structures usually those containing the maximum number of base pairs. Thanks to the chaperone activity, NC plays an essential role in reverse transcription of the retroviral genome by facilitating the strand transfer reactions of this process. In addition, these reactions are involved in recombination events that can generate multiple drug resistance mutations in the presence of anti-HIV-1 drugs. The strand transfer reactions rely on base pairing of folded DNA/RNA structures. The molecular mechanisms responsible for NC-mediated strand transfer reactions are presented and discussed in this review. Antiretroviral strategies targeting the NC-mediated strand transfer events are also discussed.
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Affiliation(s)
- Brigitte René
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Olivier Mauffret
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Philippe Fossé
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
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Naidu BN, Sorenson ME, Patel M, Ueda Y, Banville J, Beaulieu F, Bollini S, Dicker IB, Higley H, Lin Z, Pajor L, Parker DD, Terry BJ, Zheng M, Martel A, Meanwell NA, Krystal M, Walker MA. Synthesis and evaluation of C2-carbon-linked heterocyclic-5-hydroxy-6-oxo-dihydropyrimidine-4-carboxamides as HIV-1 integrase inhibitors. Bioorg Med Chem Lett 2014; 25:717-20. [PMID: 25529736 DOI: 10.1016/j.bmcl.2014.11.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
Integration of viral DNA into the host cell genome is an obligatory process for successful replication of HIV-1. Integrase catalyzes the insertion of viral DNA into the target DNA and is a validated target for drug discovery. Herein, we report the synthesis, antiviral activity and pharmacokinetic profiles of several C2-carbon-linked heterocyclic pyrimidinone-4-carboxamides that inhibit the strand transfer step of the integration process.
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Affiliation(s)
- B Narasimhulu Naidu
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA.
| | - Margaret E Sorenson
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Manoj Patel
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Yasutsugu Ueda
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Jacques Banville
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Francis Beaulieu
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Sagarika Bollini
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ira B Dicker
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Helen Higley
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Zeyu Lin
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Lori Pajor
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Dawn D Parker
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Brian J Terry
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ming Zheng
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Alain Martel
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Mark Krystal
- Department of Virology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Michael A Walker
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
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Mbemba G, Henry E, Delelis O, Bouger MC, Buckle M, Mouscadet JF, Hazan U, Leh H, Bury-Moné S. Biochemical properties of the xenotropic murine leukemia virus-related virus integrase. Biochimie 2014; 107 Pt B:300-9. [PMID: 25260582 DOI: 10.1016/j.biochi.2014.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 09/15/2014] [Indexed: 11/20/2022]
Abstract
Xenotropic Murine Leukemia Virus-related Virus (XMRV) is a new gammaretrovirus generated by genetic recombination between two murine endogenous retroviruses, PreXMRV1 and PreXMRV2, during passaging of human prostate cancer xenografts in laboratory mice. XMRV is representative of an early founder virus that jumps species from mouse to human cell lines. Relatively little information is available concerning the XMRV integrase (IN), an enzyme that catalyzes a key stage in the retroviral cycle, and whose sequence is conserved among replication competent retroviruses emerging from recombination between the murine endogenous PreXMRV-1 and PreXMRV-2 genomes. Previous studies have shown that IN inhibitors efficiently block XMRV multiplication in cells. We thus aimed at characterizing the biochemical properties and sensitivity of the XMRV IN to the raltegravir, dolutegravir, 118-D-24 and elvitegravir inhibitors in vitro. We report for the first time the purification and enzymatic characterization of recombinant XMRV IN. This IN, produced in Escherichia coli and purified under native conditions, is optimally active over a pH range of 7-8.5, in the presence of Mg(2+) (15 mM and 30 mM for 3'-processing and strand transfer, respectively) and is poorly sensitive to the addition of dithiothreitol. Raltegravir was shown to be a very potent inhibitor (IC50 ∼ 30 nM) whereas dolutegravir and elvitegravir were less effective (IC50 ∼ 230 nM and 650 nM, respectively). The 118-D-24 drug had no impact on XMRV IN activity. Interestingly, the substrate specificity of XMRV IN seems to be less marked compared to HIV-1 IN since XMRV IN is able to process various donor substrates that share little homology. Finally, our analysis revealed some original properties of the XMRV IN such as its relatively low sequence specificity.
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Patel RV, Keum YS, Park SW. Sketching the historical development of pyrimidones as the inhibitors of the HIV integrase. Eur J Med Chem 2015; 97:649-63. [PMID: 25084622 DOI: 10.1016/j.ejmech.2014.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 12/14/2022]
Abstract
Heterocyclic substances perform a very unique role in drug design and discovery. This article provides the primary objectives of the analysis within pyrimidine centered new heterocyclic elements chronologically from their finding focusing on one of the essential enzyme of HIV virus particle that is integrase upon suppressing its strand transfer function. The class of compounds reviewed here includes bicyclic pyrimidines, dihydroxypyrimidines, pyrimidine-2,4-dinones, N-methylpyrimidones, pyranopyrimidine, pyridine-quinoline conjugates, pyrimidine-2-carboxamides, N-3 hydroxylated pyrimidine-2,4-diones as well as their various substituted analogues. Such initiatives released an effective drug Raltegravir as a first FDA approved anti-HIV integrase inhibitor as well as several of its derivatives along with other pyrimidones is under clinical or preclinical growth. Some of the provided scaffolds indicated dual anti-HIV efficacies against HIV reverse transcriptase and integrase enzymes at both cites as 3'-processing and strand transfer, while several scaffolds exhibited potency against Raltegravir resistant HIV mutant strains determining themselves a potent class of compounds having appealing upcoming implementations. Connections of the new compounds' molecular structure and HIV viral target has been overviewed to be able to accomplish further growth of promising anti-HIV agents in future drug discovery process.
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Li BW, Zhang FH, Serrao E, Chen H, Sanchez TW, Yang LM, Neamati N, Zheng YT, Wang H, Long YQ. Design and discovery of flavonoid-based HIV-1 integrase inhibitors targeting both the active site and the interaction with LEDGF/p75. Bioorg Med Chem 2014; 22:3146-58. [PMID: 24794743 DOI: 10.1016/j.bmc.2014.04.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 11/19/2022]
Abstract
HIV integrase (IN) is an essential enzyme for the viral replication. Currently, three IN inhibitors have been approved for treating HIV-1 infection. All three drugs selectively inhibit the strand transfer reaction by chelating a divalent metal ion in the enzyme active site. Flavonoids are a well-known class of natural products endowed with versatile biological activities. Their β-ketoenol or catechol structures can serve as a metal chelation motif and be exploited for the design of novel IN inhibitors. Using the metal chelation as a common pharmacophore, we introduced appropriate hydrophobic moieties into the flavonol core to design natural product-based novel IN inhibitors. We developed selective and efficient syntheses to generate a series of mono 3/5/7/3'/4'-substituted flavonoid derivatives. Most of these new compounds showed excellent HIV-1 IN inhibitory activity in enzyme-based assays and protected against HIV-1 infection in cell-based assays. The 7-morpholino substituted 7c showed effective antiviral activity (EC50=0.826 μg/mL) and high therapeutic index (TI>242). More significantly, these hydroxyflavones block the IN-LEDGF/p75 interaction with low- to sub-micromolar IC50 values and represent a novel scaffold to design new generation of drugs simultaneously targeting the catalytic site as well as protein-protein interaction domains.
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Affiliation(s)
- Bo-Wen Li
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Feng-Hua Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Erik Serrao
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Huan Chen
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Tino W Sanchez
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Liu-Meng Yang
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nouri Neamati
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
| | - Yong-Tang Zheng
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hui Wang
- School of Chemistry and Environment, South China Normal University, Guangzhou 510006, China.
| | - Ya-Qiu Long
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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