1
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Zhou J, Wang X, Jia M, He X, Pan H, Chen J. Ultrafast spectroscopy study of DNA photophysics after proflavine intercalation. J Chem Phys 2024; 160:124305. [PMID: 38526107 DOI: 10.1063/5.0194608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Proflavine (PF), an acridine DNA intercalating agent, has been widespread applied as an anti-microbial and topical antiseptic agent due to its ability to suppress DNA replication. On the other hand, various studies show that PF intercalation to DNA can increase photogenotoxicity and has potential chances to induce carcinomas of skin appendages. However, the effects of PF intercalation on the photophysical and photochemical properties of DNA have not been sufficiently explored. In this study, the excited state dynamics of the PF intercalated d(GC)9 • d(GC)9 and d(AT)9 • d(AT)9 DNA duplex are investigated in an aqueous buffer solution. Under 267 nm excitation, we observed ultrafast charge transfer (CT) between PF and d(GC)9 • d(GC)9 duplex, generating a CT state with an order of magnitude longer lifetime compared to that of the intrinsic excited state reported for the d(GC)9 • d(GC)9 duplex. In contrast, no excited state interaction was detected between PF and d(AT)9 • d(AT)9. Nevertheless, a localized triplet state with a lifetime over 5 µs was identified in the PF-d(AT)9 • d(AT)9 duplex.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xiaoxiao He
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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2
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Qi L, Zhang J, Gao Y, Gong P, Liang C, Su Y, Zeng Q, Zhang Y. Peptide-RNA complexation-induced fluorescence "turn on" displacement assay for the recognition of small ligands targeting HIV-1 RNA. J Pharm Anal 2022; 12:923-928. [PMID: 36605574 PMCID: PMC9805967 DOI: 10.1016/j.jpha.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 01/07/2023] Open
Abstract
The regulator of expression of virion (Rev) protein binds specifically to the Rev-responsive element (RRE) RNA in order to regulate the expression of the human immunodeficiency virus (HIV)-1 genes. Fluorescence indicator displacement assays have been used to identify ligands that can inhibit the Rev-RRE interaction; however, the small fluorescence indicators cannot fully replace the Rev peptide or protein. As a result, a single rhodamine B labeled Rev (RB-Rev) model peptide was utilized in this study to develop a direct and efficient Rev-RRE inhibitor screening model. Due to photon-induced electron transfer quenching of the tryptophan residue on the RB fluorophore, the fluorescence of RB in Rev was weakened and could be dramatically reactivated by interaction with RRE RNA in ammonium acetate buffer (approximately six times). The interaction could reduce the electron transfer between tryptophan and RB, and RRE could also increase RB fluorescence. The inhibitor screening model was evaluated using three known positive Rev-RRE inhibitors, namely, proflavin, 6-chloro-9-[3-(2-chloroethylamino)propylamino]-2-methoxyacridine (ICR 191), and neomycin, as well as a negative drug, arginine. With the addition of the positive drugs, the fluorescence of the Rev-RRE decreased, indicating the displacement of RB-Rev. This was confirmed using atomic force microscopy (AFM) and the fluorescence was essentially unaffected by the addition of arginine. The results demonstrated that RB-Rev can be used as a fluorescent probe for recognizing small ligands that target RRE RNA. The Rev-RRE inhibitor screening model offers a novel approach to evaluating and identifying long-acting Rev inhibitors.
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Affiliation(s)
- Liang Qi
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China,Corresponding author.
| | - Jiayun Zhang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Ying Gao
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Pin Gong
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Chengyuan Liang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yao Su
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Qiao Zeng
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yafeng Zhang
- Xi'an Institute for Food and Drug Control, Xi'an, 710054, China
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3
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Almehmadi LM, Valsangkar VA, Halvorsen K, Zhang Q, Sheng J, Lednev IK. Surface-enhanced Raman spectroscopy for drug discovery: peptide-RNA binding. Anal Bioanal Chem 2022; 414:6009-6016. [PMID: 35764806 PMCID: PMC9404289 DOI: 10.1007/s00216-022-04190-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 11/01/2022]
Abstract
The ever-growing demand for new drugs highlights the need to develop novel cost- and time-effective techniques for drug discovery. Surface-enhanced Raman spectroscopy (SERS) is an emerging ultrasensitive and label-free technique that allows for the efficient detection and characterization of molecular interactions. We have recently developed a SERS platform for detecting a single protein molecule linked to a gold substrate (Almehmadi et al. Scientific Reports 2019). In this study, we extended the approach to probe the binding of potential drugs to RNA targets. To demonstrate the proof of concept, two 16-amino acid residue peptides with close primary structures and different binding affinities to the RNA CUG repeat related to myotonic dystrophy were tested. Three-microliter solutions of the RNA repeat with these peptides at nanomolar concentrations were probed using the developed approach, and the binding of only one peptide was demonstrated. The SER spectra exhibited significant fluctuations along with a sudden strong enhancement as spectra were collected consecutively from individual spots. Principal component analysis (PCA) of the SER spectral datasets indicated that free RNA repeats could be differentiated from those complexed with a peptide with 100% accuracy. The developed SERS platform provides a novel opportunity for label-free screening of RNA-binding peptides for drug discovery. Schematic representation of the SERS platform for drug discovery developed in this study.
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Affiliation(s)
- Lamyaa M Almehmadi
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA.,College of Arts and Science, RNA Institute, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Vibhav A Valsangkar
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA.,College of Arts and Science, RNA Institute, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Ken Halvorsen
- College of Arts and Science, RNA Institute, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Qiang Zhang
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA. .,College of Arts and Science, RNA Institute, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA.
| | - Igor K Lednev
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA. .,College of Arts and Science, RNA Institute, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA.
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4
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Crespo R, Rao S, Mahmoudi T. HibeRNAtion: HIV-1 RNA Metabolism and Viral Latency. Front Cell Infect Microbiol 2022; 12:855092. [PMID: 35774399 PMCID: PMC9237370 DOI: 10.3389/fcimb.2022.855092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/10/2022] [Indexed: 01/12/2023] Open
Abstract
HIV-1 infection remains non-curative due to the latent reservoir, primarily a small pool of resting memory CD4+ T cells bearing replication-competent provirus. Pharmacological reversal of HIV-1 latency followed by intrinsic or extrinsic cell killing has been proposed as a promising strategy to target and eliminate HIV-1 viral reservoirs. Latency reversing agents have been extensively studied for their role in reactivating HIV-1 transcription in vivo, although no permanent reduction of the viral reservoir has been observed thus far. This is partly due to the complex nature of latency, which involves strict intrinsic regulation at multiple levels at transcription and RNA processing. Still, the molecular mechanisms that control HIV-1 latency establishment and maintenance have been almost exclusively studied in the context of chromatin remodeling, transcription initiation and elongation and most known LRAs target LTR-driven transcription by manipulating these. RNA metabolism is a largely understudies but critical mechanistic step in HIV-1 gene expression and latency. In this review we provide an update on current knowledge on the role of RNA processing mechanisms in viral gene expression and latency and speculate on the possible manipulation of these pathways as a therapeutic target for future cure studies.
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Affiliation(s)
- Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
- *Correspondence: Tokameh Mahmoudi,
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5
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Das A, Banik BK. Advances in heterocycles as DNA intercalating cancer drugs. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The insertion of a molecule between the bases of DNA is known as intercalation. A molecule is able to interact with DNA in different ways. DNA intercalators are generally aromatic, planar, and polycyclic. In chemotherapeutic treatment, to suppress DNA replication in cancer cells, intercalators are used. In this article, we discuss the anticancer activity of 10 intensively studied DNA intercalators as drugs. The list includes proflavine, ethidium bromide, doxorubicin, dactinomycin, bleomycin, epirubicin, mitoxantrone, ellipticine, elinafide, and echinomycin. Considerable structural diversities are seen in these molecules. Besides, some examples of the metallo-intercalators are presented at the end of the chapter. These molecules have other crucial properties that are also useful in the treatment of cancers. The successes and limitations of these molecules are also presented.
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Affiliation(s)
- Aparna Das
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
| | - Bimal Krishna Banik
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
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6
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Chakraborty B, Kar A, Chanda R, Jana U. Application of the Povarov Reaction in Biaryls under Iron Catalysis for the General Synthesis of Dibenzo[ a, c]Acridines. J Org Chem 2020; 85:9281-9289. [PMID: 32588630 DOI: 10.1021/acs.joc.0c01300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A modified Povarov reaction involving 2'-alkynylbiaryl-2-carbaldehydes and aryl amines with tandem oxidation was performed using catalytic FeCl3. The outcome was an efficient general synthesis of dibenzo[a,c]acridines with moderate to high yields. This method offers simplicity in the preparation of substrates, diverse substrate scope, and high atom economy. The generality of the protocol was verified by synthesizing a tribenzo[a,c,h]acridine derivative. Photophysical properties of the synthesized compounds were also studied. The compounds absorb UV light typically in the range 230-330 nm and emit in the visible range of 400-420 nm.
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Affiliation(s)
- Baitan Chakraborty
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Abhishek Kar
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Rupsa Chanda
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Umasish Jana
- Department of Chemistry, Jadavpur University, Kolkata 700032, West Bengal, India
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7
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Janke S, Boldt S, Ghazargan K, Ehlers P, Villinger A, Langer P. Synthesis of Benzoacridines and Benzophenanthridines by Regioselective Pd-Catalyzed Cross-Coupling Reactions Followed by Acid-Mediated Cycloisomerizations. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900913] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sophie Janke
- Institute of Chemistry; University Rostock; Albert-Einstein-Str. 3a 18059 Rostock Germany
| | - Sebastian Boldt
- Institute of Chemistry; University Rostock; Albert-Einstein-Str. 3a 18059 Rostock Germany
| | - Karapet Ghazargan
- Institute of Chemistry; Yerevan State University; 1 Alek Manukyan St 0025 Yerevan Armenia
| | - Peter Ehlers
- Institute of Chemistry; University Rostock; Albert-Einstein-Str. 3a 18059 Rostock Germany
- Leibniz Institute for Catalysis at the University of Rostock e.V. (LIKAT); Albert-Einstein-Str. 29a 18059 Rostock Germany
| | - Alexander Villinger
- Institute of Chemistry; University Rostock; Albert-Einstein-Str. 3a 18059 Rostock Germany
| | - Peter Langer
- Institute of Chemistry; University Rostock; Albert-Einstein-Str. 3a 18059 Rostock Germany
- Leibniz Institute for Catalysis at the University of Rostock e.V. (LIKAT); Albert-Einstein-Str. 29a 18059 Rostock Germany
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8
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Wicks SL, Hargrove AE. Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA. Methods 2019; 167:3-14. [PMID: 31051253 DOI: 10.1016/j.ymeth.2019.04.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/15/2023] Open
Abstract
Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increasing interest as the roles of RNA in cellular processes and disease pathogenesis continue to be discovered. Small molecules have been validated as tools to elucidate unknown RNA functions, underscoring the critical need to rapidly identify and quantitatively characterize RNA:small molecule interactions for the development of chemical probes. The successful application of FID assays to evaluate interactions between diverse RNA receptors and small molecules has been facilitated by the characterization of distinct fluorescent indicators that reversibly bind RNA and modulate the fluorescence signal. The utility of RNA-based FID assays to both academia and industry has been demonstrated through numerous uses in high-throughput screening efforts, structure-activity relationship studies, and in vitro target engagement studies. Furthermore, the development, optimization, and validation of a variety of RNA-based FID assays has led to general guidelines that can be utilized for facile implementation of the method with new or underexplored RNA receptors. Altogether, the use of RNA-based FID assays as a general analysis tool has provided valuable insights into small molecule affinity and selectivity, furthering the fundamental understanding of RNA:small molecule recognition. In this review, we will summarize efforts to employ FID assays using RNA receptors and describe the significant contributions of the method towards the development of chemical probes to reveal unknown RNA functions.
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Affiliation(s)
- Sarah L Wicks
- Duke University, Department of Chemistry, Durham, NC 27705, United States
| | - Amanda E Hargrove
- Duke University, Department of Chemistry, Durham, NC 27705, United States.
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9
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Jin B, Sung GW, Jang YJ. Binding mode of proflavine to DNA probed by polarized light spectroscopy. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Biao Jin
- Instrumental Analysis CenterYanbian University Yanji City Jilin Province China
| | - Gi Woong Sung
- Department of ChemistryYeungnam University Dae‐dong Gyeongsan City Gyeong‐buk Republic of Korea
| | - Yoon Jung Jang
- College of Basic Education, Yeungnam University Dae‐dong Gyeongsan City Gyeong‐buk Republic of Korea
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10
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Yan L, Li Q, Xu H, Xu Z, Yu Q, Qin Y, Rong L. An efficient in-situ reduction and cyclization reaction for the synthesis of 9-aryl-1,6,8,9-tetrahydro-7 H -pyrazolo[3,4- f ]quinolin-7-one, 11-aryl-1,6,7,8,9,11-hexahydro-10 H -pyrazolo [3,4- a ]acridin-10-one, and 11-aryl-3,6,7,8,9,11-hexahydro-10 H -imidazo[4,5- a ]acridin-10-one derivatives. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.10.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Mu WL, Wang M, Li HJ, Huang DM, Zhang YY, Li CY, Liu Y, Wu YC. Palladium-Catalyzed Regioselective Oxidative Annulation of Cyclohexanones and 2-Aminophenyl Ketones Using Molecular Oxygen as the Sole Oxidant. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700715] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wan-Lu Mu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Meirong Wang
- School of Materials Science and Engineering; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Hui-Jing Li
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Deng-Ming Huang
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Yi-Yun Zhang
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Chao-Yi Li
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Ying Liu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Yan-Chao Wu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
- Beijing National Laboratory for Molecular Sciences (BNLMS); Institute of Chemistry Chinese Academy of Sciences; Beijing 100190 People's Republic of China
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12
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Identification and Optimization of Thienopyridine Carboxamides as Inhibitors of HIV Regulatory Complexes. Antimicrob Agents Chemother 2017; 61:AAC.02366-16. [PMID: 28416550 DOI: 10.1128/aac.02366-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/06/2017] [Indexed: 12/28/2022] Open
Abstract
Viral regulatory complexes perform critical functions during virus replication and are important targets for therapeutic intervention. In HIV, the Tat and Rev proteins form complexes with multiple viral and cellular factors to direct transcription and export of the viral RNA. These complexes are composed of many proteins and are dynamic, making them difficult to fully recapitulate in vitro Therefore, we developed a cell-based reporter assay to monitor the assembly of viral complexes for inhibitor screening. We screened a small-molecule library and identified multiple hits that inhibit the activity of the viral complexes. A subsequent chemistry effort was focused on a thieno[2,3-b]pyridine scaffold, examples of which inhibited HIV replication and the emergence from viral latency. Notable aspects of the effort to determine the structure-activity relationship (SAR) include migration to the regioisomeric thieno[2,3-c]pyridine ring system and the identification of analogs with single-digit nanomolar activity in both reporter and HIV infectivity assays, an improvement of >100-fold in potency over the original hits. These results validate the screening strategy employed and reveal a promising lead series for the development of a new class of HIV therapeutics.
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13
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Jeong WJ, Kye M, Han SH, Choi JS, Lim YB. Inhibition of Multimolecular RNA-Protein Interactions Using Multitarget-Directed Nanohybrid System. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11537-11545. [PMID: 28287257 DOI: 10.1021/acsami.7b01517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Multitarget-directed ligands (MTDLs) are hybrid ligands obtained by covalently linking active pharmacophores that can act on different targets. We envision that the concept of MTDLs can also be applied to supramolecular bioinorganic nanohybrid systems. Here, we report the inhibition of multimolecular RNA-protein complexes using multitarget-directed peptide-carbon nanotube hybrids (SPCHs). One of the most well-characterized and important RNA-protein interactions, a Rev-response element (RRE) RNA:Rev protein:Crm1 protein interaction system in human immunodeficiency virus type-1, was used as a model of multimolecular RNA-protein interactions. Although all previous studies have targeted only one of the interaction interfaces, that is, either the RRE:Rev interface or the RRE-Rev complex:Crm1 interface, we here have developed multitarget-directed SPCHs that could target both interfaces because the supramolecular nanosystem could be best suited for inhibiting multimolecular RNA-protein complexes that are characterized by large and complex molecular interfaces. The results showed that the single target-directed SPCHs were inhibitory to the single interface comprised only of RNA and protein in vitro, whereas multitarget-directed SPCHs were inhibitory to the multimolecular RNA-protein interfaces both in vitro and in cellulo. The MTDL nanohybrids represent a novel nanotherapeutic system that could be used to treat complex disease targets.
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Affiliation(s)
- Woo-Jin Jeong
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - Mahnseok Kye
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - So-Hee Han
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - Jun Shik Choi
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - Yong-Beom Lim
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
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14
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MnO2 nanosheet-assisted ligand-DNA interaction-based fluorescence polarization biosensor for the detection of Ag+ ions. Biosens Bioelectron 2017; 87:566-571. [DOI: 10.1016/j.bios.2016.08.093] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/17/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
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15
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A ratiometric fluorescence RRE RNA-targeted assay for a new fluorescence ligand. Biosens Bioelectron 2016; 86:287-292. [DOI: 10.1016/j.bios.2016.06.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/01/2016] [Accepted: 06/18/2016] [Indexed: 11/18/2022]
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16
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Murata A, Otabe T, Zhang J, Nakatani K. BzDANP, a Small-Molecule Modulator of Pre-miR-29a Maturation by Dicer. ACS Chem Biol 2016; 11:2790-2796. [PMID: 27536863 DOI: 10.1021/acschembio.6b00214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We here report the synthesis of novel molecule BzDANP having a three-ring benzo[c][1,8]naphthyridine system, the evaluation of its binding properties to a single nucleotide bulge in RNA duplexes, and BzDANP-induced suppression of pre-miR-29a processing by Dicer. BzDANP showed much increased affinity to the bulged RNAs as compared with the parent molecule DANP, which possesses the same hydrogen-bonding surface as BzDANP but in a two-ring [1,8]naphthyridine system. Melting temperature analysis of bulged RNAs showed that BzDANP most effectively stabilized the C-bulged RNA. Dicer-mediated processing of pre-miR-29a was suppressed by BzDANP in a concentration dependent manner. The presence of the C-bulge at the Dicer cleavage site was effective for the suppression of pre-miR-29a processing by BzDANP. These results demonstrated that the small molecule binding to the bulged site in the vicinity of the Dicer cleavage site could be a potential modulator for the maturation of pre-miRNA.
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Affiliation(s)
- Asako Murata
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takahiro Otabe
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Jinhua Zhang
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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17
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Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Effect of intercalator and Lewis acid-base branched peptide complex formation: boosting affinity towards HIV-1 RRE RNA. MEDCHEMCOMM 2016; 7:1436-1440. [PMID: 27453773 DOI: 10.1039/c6md00171h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
High throughput screening of a 4096 compound library of boronic acid and acridine containing branched peptides revealed compounds that have dissociation constants in the low nanomolar regime for HIV-1 RRE IIB RNA. We demonstrate that branched peptide boronic acids A5, A6, and A7 inhibit the production of p24, an HIV-1 capsid protein, in a dose-dependent manner.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Denis M Tebit
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Laurie R Gray
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - David Rekosh
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
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18
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Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Characterization and in vitro activity of a branched peptide boronic acid that interacts with HIV-1 RRE RNA. Bioorg Med Chem 2016; 24:3947-3952. [PMID: 27091070 DOI: 10.1016/j.bmc.2016.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
A branched peptide containing multiple boronic acids was found to bind RRE IIB selectively and inhibit HIV-1 p24 capsid production in a dose-dependent manner. Structure-activity relationship studies revealed that branching in the peptide is crucial for the low micromolar binding towards RRE IIB, and the peptide demonstrates selectivity towards RRE IIB in the presence of tRNA. Footprinting studies suggest a binding site on the upper stem and internal loop regions of the RNA, which induces enzymatic cleavage of the internal loops of RRE IIB upon binding.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Denis M Tebit
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Laurie R Gray
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - David Rekosh
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
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19
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Prado S, Beltrán M, Coiras M, Bedoya LM, Alcamí J, Gallego J. Bioavailable inhibitors of HIV-1 RNA biogenesis identified through a Rev-based screen. Biochem Pharmacol 2016; 107:14-28. [PMID: 26896646 DOI: 10.1016/j.bcp.2016.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/15/2016] [Indexed: 12/23/2022]
Abstract
New antiretroviral agents with alternative mechanisms are needed to complement the combination therapies used to treat HIV-1 infections. Here we report the identification of bioavailable molecules that interfere with the gene expression processes of HIV-1. The compounds were detected by screening a small library of FDA-approved drugs with an assay based on measuring the displacement of Rev, and essential virus-encoded protein, from its high-affinity RNA binding site. The antiretroviral activity of two hits was based on interference with post-integration steps of the HIV-1 cycle. Both hits inhibited RRE-Rev complex formation in vitro, and blocked LTR-dependent gene expression and viral transcription in cellular assays. The best compound altered the splicing pattern of HIV-1 transcripts in a manner consistent with Rev inhibition. This mechanism of action is different from those used by current antiretroviral agents. The screening hits recognized the Rev binding site in the viral RNA, and the best compound did so with substantial selectivity, allowing the identification of a new RNA-binding scaffold. These results may be used for developing novel antiretroviral drugs.
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Affiliation(s)
- Silvia Prado
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Manuela Beltrán
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain
| | - Mayte Coiras
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain
| | - Luis M Bedoya
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain; Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - José Alcamí
- Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo km 2, 28220 Majadahonda, Spain.
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain.
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20
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Mahendar L, Satyanarayana G. Copper catalyzed coupling of protecting group free and sterically hindered 2-bromobenzyl tertiary alcohols with phenols and anilines: facile synthesis of xanthenes and dihydroacridines. RSC Adv 2016. [DOI: 10.1039/c6ra03447k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Protecting group free and sterically hindered tertiary alcohols used in coupling reaction. Two-step process with a single column chromatography. Synthesis of interesting xanthenes and dihydroacridines.
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Affiliation(s)
- Lodi Mahendar
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
| | - Gedu Satyanarayana
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
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21
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Wynn JE, Santos WL. HIV-1 drug discovery: targeting folded RNA structures with branched peptides. Org Biomol Chem 2015; 13:5848-58. [PMID: 25958855 PMCID: PMC4511164 DOI: 10.1039/c5ob00589b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.
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Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA.
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22
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Wang TJ, Chen WW, Li Y, Xu MH. Facile synthesis of acridines via Pd(0)-diphosphine complex-catalyzed tandem coupling/cyclization protocol. Org Biomol Chem 2015; 13:6580-6. [PMID: 25982344 DOI: 10.1039/c5ob00755k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile and efficient approach for the synthesis of a variety of acridines via the tandem coupling/cyclization of substituted 2-bromobenzaldehydes and anilines is described. The reaction can be accomplished with ease in the presence of a catalytic amount of Pd2(dba)3 and diphosphine ligand dppf, providing a broad range of substituted acridines in good to excellent yields (up to 99%). The Lewis acid, AlCl3, is required to promote the cyclization for less electron-rich anilines.
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Affiliation(s)
- Ting-Jun Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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23
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Prieto SP, Powless AJ, Boice JW, Sharma SG, Muldoon TJ. Proflavine Hemisulfate as a Fluorescent Contrast Agent for Point-of-Care Cytology. PLoS One 2015; 10:e0125598. [PMID: 25962131 PMCID: PMC4427403 DOI: 10.1371/journal.pone.0125598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/24/2015] [Indexed: 11/19/2022] Open
Abstract
Proflavine hemisulfate, an acridine-derived fluorescent dye, can be used as a rapid stain for cytologic examination of biological specimens. Proflavine fluorescently stains cell nuclei and cytoplasmic structures, owing to its small amphipathic structure and ability to intercalate DNA. In this manuscript, we demonstrated the use of proflavine as a rapid cytologic dye on a number of specimens, including normal exfoliated oral squamous cells, cultured human oral squamous carcinoma cells, and leukocytes derived from whole blood specimens using a custom-built, portable, LED-illuminated fluorescence microscope. No incubation time was needed after suspending cells in 0.01% (w/v) proflavine diluted in saline. Images of proflavine stained oral cells had clearly visible nuclei as well as granular cytoplasm, while stained leukocytes exhibited bright nuclei, and highlighted the multilobar nature of nuclei in neutrophils. We also demonstrated the utility of quantitative analysis of digital images of proflavine stained cells, which can be used to detect significant morphological differences between different cell types. Proflavine stained oral cells have well-defined nuclei and cell membranes which allowed for quantitative analysis of nuclear to cytoplasmic ratios, as well as image texture analysis to extract quantitative image features.
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Affiliation(s)
- Sandra P. Prieto
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
| | - Amy J. Powless
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
| | - Jackson W. Boice
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
| | - Shree G. Sharma
- 10810 Executive Center Dr., Nephropath Ste. 100, Little Rock, Arkansas 72211, United States of America
| | - Timothy J. Muldoon
- Biomedical Engineering Department, University of Arkansas, Fayetteville, Arkansas 72701, United States of America
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24
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Campos N, Myburgh R, Garcel A, Vautrin A, Lapasset L, Nadal ES, Mahuteau-Betzer F, Najman R, Fornarelli P, Tantale K, Basyuk E, Séveno M, Venables JP, Pau B, Bertrand E, Wainberg MA, Speck RF, Scherrer D, Tazi J. Long lasting control of viral rebound with a new drug ABX464 targeting Rev - mediated viral RNA biogenesis. Retrovirology 2015; 12:30. [PMID: 25889234 PMCID: PMC4422473 DOI: 10.1186/s12977-015-0159-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/24/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Current therapies have succeeded in controlling AIDS pandemic. However, there is a continuing need for new drugs, in particular those acting through new and as yet unexplored mechanisms of action to achieve HIV infection cure. We took advantage of the unique feature of proviral genome to require both activation and inhibition of splicing of viral transcripts to develop molecules capable of achieving long lasting effect on viral replication in humanized mouse models through inhibition of Rev-mediated viral RNA biogenesis. RESULTS Current HIV therapies reduce viral load during treatment but titers rebound after treatment is discontinued. We devised a new drug that has a long lasting effect after viral load reduction. We demonstrate here that ABX464 compromises HIV replication of clinical isolates of different subtypes without selecting for drug resistance in PBMCs or macrophages. ABX464 alone, also efficiently compromised viral proliferation in two humanized mouse models infected with HIV that require a combination of 3TC, Raltegravir and Tenofovir (HAART) to achieve viral inhibition in current protocols. Crucially, while viral load increased dramatically just one week after stopping HAART treatment, only slight rebound was observed following treatment cessation with ABX464 and the magnitude of the rebound was maintained below to that of HAART for two months after stopping the treatment. Using a system to visualize single HIV RNA molecules in living cells, we show that ABX464 inhibits viral replication by preventing Rev-mediated export of unspliced HIV-1 transcripts to the cytoplasm and by interacting with the Cap Binding Complex (CBC). Deep sequencing of viral RNA from treated cells established that retained viral RNA is massively spliced but importantly, normal cellular splicing is unaffected by the drug. Consistently ABX464 is non-toxic in humans and therefore represents a promising complement to current HIV therapies. CONCLUSIONS ABX464 represents a novel class of anti-HIV molecules with unique properties. ABX464 has a long lasting effect in humanized mice and neutralizes the expression of HIV-1 proviral genome of infected immune cells including reservoirs and it is therefore a promising drug toward a functional cure of HIV.
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Affiliation(s)
- Noëlie Campos
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Renier Myburgh
- Division of Infectious Diseases and Hospital Epidemiology Department of Internal Medicin, University of Zurich, University Hospital, Raemistrasse 100, 8091, Zurich, Switzerland.
| | - Aude Garcel
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Audrey Vautrin
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Laure Lapasset
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Erika Schläpfer Nadal
- Division of Infectious Diseases and Hospital Epidemiology Department of Internal Medicin, University of Zurich, University Hospital, Raemistrasse 100, 8091, Zurich, Switzerland.
| | - Florence Mahuteau-Betzer
- Institut Curie, CNRS UMR9187, INSERM U1196, Centre universitaire, Bâtiment 110, 15 rue Georges Clémenceau, 91405, ORSAY CEDEX, France.
| | - Romain Najman
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | | | - Katjana Tantale
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Eugénia Basyuk
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Martial Séveno
- Plate-forme de Protéomique Fonctionnelle (FPP) IGF, UMR 5203 CNRS - INSERM U661- UM, 141 rue de la Cardonille (pièce 029), 34094, Montpellier CEDEX 05, France.
| | - Julian P Venables
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Bernard Pau
- Université de Montpellier, UFR Pharmacie, 15 Avenue Charles Flahault, 34000, Montpellier, France.
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Mark A Wainberg
- McGill AIDS Center, Lady Davis Institute - Jewish General Hospital, Montréal, QC, Canada.
| | - Roberto F Speck
- Division of Infectious Diseases and Hospital Epidemiology Department of Internal Medicin, University of Zurich, University Hospital, Raemistrasse 100, 8091, Zurich, Switzerland.
| | - Didier Scherrer
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Jamal Tazi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
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25
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Mahboobi SH, Javanpour AA, Mofrad MRK. The interaction of RNA helicase DDX3 with HIV-1 Rev-CRM1-RanGTP complex during the HIV replication cycle. PLoS One 2015; 10:e0112969. [PMID: 25723178 PMCID: PMC4344243 DOI: 10.1371/journal.pone.0112969] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 10/17/2014] [Indexed: 01/17/2023] Open
Abstract
Molecular traffic between the nucleus and the cytoplasm is regulated by the nuclear pore complex (NPC), which acts as a highly selective channel perforating the nuclear envelope in eukaryotic cells. The human immunodeficiency virus (HIV) exploits the nucleocytoplasmic pathway to export its RNA transcripts across the NPC to the cytoplasm. Despite extensive study on the HIV life cycle and the many drugs developed to target this cycle, no current drugs have been successful in targeting the critical process of viral nuclear export, even though HIV's reliance on a single host protein, CRM1, to export its unspliced and partially spliced RNA transcripts makes it a tempting target. Due to recent findings implicating a DEAD-box helicase, DDX3, in HIV replication and a member of the export complex, it has become an appealing target for anti-HIV drug inhibition. In the present research, we have applied a hybrid computational protocol to analyze protein-protein interactions in the HIV mRNA export cycle. This method is based on molecular docking followed by molecular dynamics simulation and accompanied by approximate free energy calculation (MM/GBSA), computational alanine scanning, clustering, and evolutionary analysis. We highlight here some of the most likely binding modes and interfacial residues between DDX3 and CRM1 both in the absence and presence of RanGTP. This work shows that although DDX3 can bind to free CRM1, addition of RanGTP leads to more concentrated distribution of binding modes and stronger binding between CRM1 and RanGTP.
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Affiliation(s)
- Seyed Hanif Mahboobi
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America
| | - Alex A. Javanpour
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America
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26
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Qin Z, Li X, Zhou M. A Theoretical Study on Hydrogen-Bonded Complex of Proflavine Cation and Water: The Site-dependent Feature of Hydrogen Bond Strengthening and Weakening. J CHIN CHEM SOC-TAIP 2014. [DOI: 10.1002/jccs.201400089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Human Immunodeficiency Virus Type 1 Tat and Rev as Potential Targets for Drug Development. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Zhang W, Bryson DI, Crumpton JB, Wynn J, Santos WL. Targeting folded RNA: a branched peptide boronic acid that binds to a large surface area of HIV-1 RRE RNA. Org Biomol Chem 2014; 11:6263-71. [PMID: 23925474 DOI: 10.1039/c3ob41053f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On-bead high-throughput screening of a medium-sized (1000-2000 Da) branched peptide boronic acid (BPBA) library consisting of 46,656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a K(d) of 1.4 μM with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure-activity studies suggest that the boronic acid moiety and "branching" in peptides are key structural features for efficient binding and selectivity for the folded RNA target. BPBA1 was efficiently taken up by HeLa and A2780 cells. RNA-footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB.
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Affiliation(s)
- Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA
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29
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Raina S, Chande AG, Baba M, Mukhopadhyaya R. A reporter based single step assay for evaluation of inhibitors targeting HIV-1 Rev-RRE interaction. Virusdisease 2014; 25:101-6. [PMID: 24426316 DOI: 10.1007/s13337-013-0166-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 09/17/2013] [Indexed: 11/26/2022] Open
Abstract
Human immunodeficiency virus regulatory protein Rev (regulator of viral expression) is translated from a monocistronic transcript produced early in the viral replication cycle. Rev binds to the cis-acting, highly structured viral RNA sequence Rev response element (RRE) and the Rev-RRE complex primarily controls nucleocytoplasmic transport of viral RNAs. Inhibition of Rev-RRE interaction therefore is an attractive target to block viral transport. We have developed a stable cell line carrying a lentiviral vector harboring a rev gene and a co-linear Rev-dependent GFP/luciferase reporter gene cassette and thus constitutively expressing the reporter proteins. Dose-dependent luciferase activity inhibition in the indicator cell line by known small molecule inhibitors Proflavin and K37 established the specificity of the assay. This novel single step assay, that involves use of very small amount of reagents/cells and addition of test material as the only manipulation, can therefore be useful for screening therapeutically potential Rev-RRE interaction inhibitors.
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Affiliation(s)
- Sumeer Raina
- Virology Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410 210 India
| | - Ajit G Chande
- Virology Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410 210 India ; Immunology Group, ICGEB, New Delhi, India
| | - Masanori Baba
- Center for Chronic Viral Diseases, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Robin Mukhopadhyaya
- Virology Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410 210 India
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30
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Guo HM, Mao RZ, Wang QT, Niu HY, Xie MS, Qu GR. Pd(II)-Catalyzed One-Pot, Three-Step Route for the Synthesis of Unsymmetrical Acridines. Org Lett 2013; 15:5460-3. [DOI: 10.1021/ol402596g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hai-Ming Guo
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Run-Ze Mao
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qiao-Tian Wang
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Hong-Ying Niu
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ming-Sheng Xie
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Gui-Rong Qu
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
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31
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Sasikala WD, Mukherjee A. Intercalation and de-intercalation pathway of proflavine through the minor and major grooves of DNA: roles of water and entropy. Phys Chem Chem Phys 2013; 15:6446-55. [DOI: 10.1039/c3cp50501d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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32
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Drug-DNA intercalation: from discovery to the molecular mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:1-62. [PMID: 23954098 DOI: 10.1016/b978-0-12-411636-8.00001-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ability of small molecules to perturb the natural structure and dynamics of nucleic acids is intriguing and has potential applications in cancer therapeutics. Intercalation is a special binding mode where the planar aromatic moiety of a small molecule is inserted between a pair of base pairs, causing structural changes in the DNA and leading to its functional arrest. Enormous progress has been made to understand the nature of the intercalation process since its idealistic conception five decades ago. However, the biological functions were detected even earlier. In this review, we focus mainly on the acridine and anthracycline types of drugs and provide a brief overview of the development in the field through various experimental methods that led to our present understanding of the subject. Subsequently, we discuss the molecular mechanism of the intercalation process, free-energy landscapes, and kinetics that was revealed recently through detailed and rigorous computational studies.
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33
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Pai J, Yoon T, Kim ND, Lee IS, Yu J, Shin I. High-throughput profiling of peptide-RNA interactions using peptide microarrays. J Am Chem Soc 2012; 134:19287-96. [PMID: 23110629 DOI: 10.1021/ja309760g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A rapid and quantitative method to evaluate binding properties of hairpin RNAs to peptides using peptide microarrays has been developed. The microarray technology was shown to be a powerful tool for high-throughput analysis of RNA-peptide interactions by its application to profiling interactions between 111 peptides and six hairpin RNAs. The peptide microarrays were also employed to measure hundreds of dissociation constants (K(d)) of RNA-peptide complexes. Our results reveal that both hydrophobic and hydrophilic faces of amphiphilic peptides are likely involved in interactions with RNAs. Furthermore, these results also show that most of the tested peptides bind hairpin RNAs with submicromolar K(d) values. One of the peptides identified by using this method was found to have good inhibitory activity against TAR-Tat interactions in cells. Because of their great applicability to evaluation of nearly all types of RNA-peptide interactions, peptide microarrays are expected to serve as robust tools for rapid assessment of peptide-RNA interactions and development of peptide ligands against RNA targets.
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Affiliation(s)
- Jaeyoung Pai
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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Blakeley BD, DePorter SM, Mohan U, Burai R, Tolbert BS, McNaughton BR. Methods for identifying and characterizing interactions involving RNA. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Sasikala WD, Mukherjee A. Molecular mechanism of direct proflavine-DNA intercalation: evidence for drug-induced minimum base-stacking penalty pathway. J Phys Chem B 2012; 116:12208-12. [PMID: 22978751 DOI: 10.1021/jp307911r] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA intercalation, a biophysical process of enormous clinical significance, has surprisingly eluded molecular understanding for several decades. With appropriate configurational restraint (to prevent dissociation) in all-atom metadynamics simulations, we capture the free energy surface of direct intercalation from minor groove-bound state for the first time using an anticancer agent proflavine. Mechanism along the minimum free energy path reveals that intercalation happens through a minimum base stacking penalty pathway where nonstacking parameters (Twist→Slide/Shift) change first, followed by base stacking parameters (Buckle/Roll→Rise). This mechanism defies the natural fluctuation hypothesis and provides molecular evidence for the drug-induced cavity formation hypothesis. The thermodynamic origin of the barrier is found to be a combination of entropy and desolvation energy.
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Affiliation(s)
- Wilbee D Sasikala
- Chemistry Department, Indian Institute of Science Education and Research, Pune-411021, India
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Kumar KS, Selvaraju C, Malar EJP, Natarajan P. Existence of a new emitting singlet state of proflavine: femtosecond dynamics of the excited state processes and quantum chemical studies in different solvents. J Phys Chem A 2011; 116:37-45. [PMID: 22145576 DOI: 10.1021/jp207495r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proflavine (3,6-diaminoacridine) shows fluorescence emission with lifetime, 4.6 ± 0.2 ns, in all the solvents irrespective of the solvent polarity. To understand this unusual photophysical property, investigations were carried out using steady state and time-resolved fluorescence spectroscopy in the pico- and femtosecond time domain. Molecular geometries in the ground and low-lying excited states of proflavine were examined by complete structural optimization using ab initio quantum chemical computations at HF/6-311++G** and CIS/6-311++G** levels. Time dependent density functional theory (TDDFT) calculations were performed to study the excitation energies in the low-lying excited states. The steady state absorption and emission spectral details of proflavine are found to be influenced by solvents. The femtosecond fluorescence decay of the proflavine in all the solvents follows triexponential function with two ultrafast decay components (τ(1) and τ(2)) in addition to the nanosecond component. The ultrafast decay component, τ(1), is attributed to the solvation dynamics of the particular solvent used. The second ultrafast decay component, τ(2), is found to vary from 50 to 215 ps depending upon the solvent. The amplitudes of the ultrafast decay components vary with the wavelength and show time dependent spectral shift in the emission maximum. The observation is interpreted that the time dependent spectral shift is not only due to solvation dynamics but also due to the existence of more than one emitting state of proflavine in the solvent used. Time resolved area normalized emission spectral (TRANES) analysis shows an isoemissive point, indicating the presence of two emitting states in homogeneous solution. Detailed femtosecond fluorescence decay analysis allows us to isolate the two independent emitting components of the close lying singlet states. The CIS and TDDFT calculations also support the existence of the close lying emitting states. The near constant lifetime observed for proflavine in different solvents is suggested to be due to the similar dipole moments of the ground and the evolved emitting singlet state of the dye from the Franck-Condon excited state.
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Affiliation(s)
- Karuppannan Senthil Kumar
- National Centre for Ultrafast Processes, Taramani Campus, University of Madras, Chennai 600 113, India
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37
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Kim SE, Ahn KY, Park JS, Kim KR, Lee KE, Han SS, Lee J. Fluorescent ferritin nanoparticles and application to the aptamer sensor. Anal Chem 2011; 83:5834-43. [PMID: 21639087 DOI: 10.1021/ac200657s] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We synthesized fluorescent ferritin nanoparticles (FFNPs) through bacterial expression of the hybrid gene consisting of human ferritin heavy chain (hFTN-H), spacer (glycine-rich peptide), and enhanced green (or red) fluorescent protein [eGFP (or DsRed)] genes. The self-assembly activity of hFTN-H that leads to the formation of nanoparticles (12 nm in diameter), the conformational flexibility of the C-terminus of hFTN-H, and the glycine-rich spacer enabled eGFPs (or DsReds) to be well displayed on the surface of each ferritin nanoparticle, resulting in the construction of green (or red) FFNPs [gFFNPs (or rFFNPs)]. As compared to eGFP (or DsRed) alone, it is notable that the developed FFNPs showed significantly amplified fluorescence intensity and also enhanced stability. DNA aptamers were chemically conjugated to gFFNP via each eGFP's cysteine residue that was newly introduced through site-directed mutagenesis (Ser175Cys). The DNA-aptamer-conjugated gFFNPs were used as a fluorescent reporter probe in the aptamer-based "sandwich" assay of a cancer marker [i.e., platelet-derived growth factor B-chain homodimer (PDGF-BB)] in phosphate-buffered saline buffer or diluted human serum. This is a simple two-step assay without any additional steps for signal amplification, showing that compared to the same aptamer-based assays using eGFP alone or Cy3, the detection signals, affinity of the reporter probe to the cancer marker, and assay sensitivity were significantly enhanced; i.e., the limit of detection was lowered to the 100 fM level. Although the PDGF-BB assay is reported here as a proof-of-concept, the developed FFNPs can be applied in general to any aptamer-based sandwich assays.
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Affiliation(s)
- Seong-Eun Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul, Republic of Korea
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Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM. Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nat Chem Biol 2011; 7:553-9. [PMID: 21706033 PMCID: PMC3319144 DOI: 10.1038/nchembio.596] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 04/18/2011] [Indexed: 11/09/2022]
Abstract
Current approaches used to identify protein-binding small molecules are not suited for identifying small molecules that can bind emerging RNA drug targets. By docking small molecules onto an RNA dynamic ensemble constructed by combining NMR spectroscopy and computational molecular dynamics, we virtually screened small molecules that target the entire structure landscape of the transactivation response element (TAR) from HIV type 1 (HIV-1). We quantitatively predict binding energies for small molecules that bind different RNA conformations and report the de novo discovery of six compounds that bind TAR with high affinity and inhibit its interaction with a Tat peptide in vitro (K(i) values of 710 nM-169 μM). One compound binds HIV-1 TAR with marked selectivity and inhibits Tat-mediated activation of the HIV-1 long terminal repeat by 81% in T-cell lines and HIV replication in an HIV-1 indicator cell line (IC(50) ∼23.1 μM).
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Affiliation(s)
- Andrew C. Stelzer
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Aaron T. Frank
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences 2, Irvine, California 92697, USA
| | - Jeremy D. Kratz
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Michael D. Swanson
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Marta J. Gonzalez-Hernandez
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Janghyun Lee
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences 2, Irvine, California 92697, USA
| | - David M. Markovitz
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Hashim M. Al-Hashimi
- Department of Chemistry & Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
- Correspondence and requests for materials should be addressed to H. M. A. ()
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Abstract
The human immunodeficiency virus (HIV), the causative agent of acquired immunodeficiency syndrome (AIDS), relies heavily on protein-protein interactions in almost every step of its lifecycle. Targeting these interactions, especially those between virus and host proteins, is increasingly viewed as an ideal avenue for the design and development of new therapeutics. In this tutorial review, we outline the lifecycle of HIV and describe some of the protein-protein interactions that control and regulate each step of this process, also detailing efforts to develop therapies that target these interactions.
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Affiliation(s)
- Ali Tavassoli
- University of Southampton, Southampton, SO17 1BJ, UK.
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40
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Wachowius F, Höbartner C. Chemical RNA modifications for studies of RNA structure and dynamics. Chembiochem 2010; 11:469-80. [PMID: 20135663 DOI: 10.1002/cbic.200900697] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Falk Wachowius
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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41
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Hyun S, Na J, Lee SJ, Park S, Yu J. RNA Grooves Can Accommodate Disulfide-Bridged Bundles of α-Helical Peptides. Chembiochem 2010; 11:767-70. [DOI: 10.1002/cbic.201000072] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
PURPOSE OF REVIEW One of the major problems in HIV chemotherapy is appearance of drug-resistant virus strains. Novel HIV intervention strategies are required and new targets must be considered. The nuclear export of intron-containing HIV-1 mRNA is an essential step in the viral replication cycle and is a prospective antiviral target. This nucleocytoplasmic transport is mediated by the viral protein Rev. Rev binds as a multimeric complex to the viral mRNA and exports it to the cytoplasm exploiting the CRM1-mediated cellular machinery. Inhibitors acting on the interface between virus and cell could overcome the problems of drug resistance against virus-specific treatments. These drugs have an added value in combination therapy as they are expected to be less prone to virus-drug resistance selection, but they are likely to be more cytotoxic. RECENT FINDINGS We will discuss the therapeutic approaches aimed at interfering with Rev function, both now and likely in the future, and the recent attempts that have been undertaken to design small molecules against this target. SUMMARY Recent approaches provide leads for development of new compounds. A better understanding of the mechanism of Rev action and its interaction with the cellular transport pathway is required to identify and rationally design novel strategies that may have potential for future antiretroviral intervention.
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An L, Liu L, Wang S, Bazan G. An Optical Approach for Drug Screening Based on Light-Harvesting Conjugated Polyelectrolytes. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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An L, Liu L, Wang S, Bazan G. An Optical Approach for Drug Screening Based on Light-Harvesting Conjugated Polyelectrolytes. Angew Chem Int Ed Engl 2009; 48:4372-5. [DOI: 10.1002/anie.200900758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Lee HW, Briggs KT, Marino JP. Dissecting structural transitions in the HIV-1 dimerization initiation site RNA using 2-aminopurine fluorescence. Methods 2009; 49:118-27. [PMID: 19460437 DOI: 10.1016/j.ymeth.2009.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/08/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022] Open
Abstract
A highly conserved 35 nucleotide RNA stem-loop, the dimerization initiation site (DIS), in the 5' untranslated region (UTR) of the human immunodeficiency virus type I (HIV-1) genome has been identified as the sequence primarily responsible for initiation of viral genome dimerization. The DIS initiates viral genome dimerization through a loop-loop 'kissing' interaction and is converted from an intermediate 'kissing' to a more thermodynamically stable extended duplex dimer in a conformational rearrangement that is chaperoned by the HIV-1 nucleocapsid protein (NCp7). Here we describe fluorescence methods designed to probe local RNA dynamics and structural transitions associated with the DIS dimer formation and its NCp7 chaperoned structural conversion. These methods take advantage of the exquisite sensitivity of the quantum yield of the fluorescent nucleotide base analog, 2-aminopurine (2-AP), to its immediate structural and dynamic environment. The 2-AP fluorescence methods described allow a detailed kinetic and thermodynamic examination of this type of RNA-RNA interaction, as well as an analysis of the molecular mechanism of NCp7 chaperone activity.
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Affiliation(s)
- Hui-Wen Lee
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, The National Institute of Standards and Technology, Rockville, MD 20850, USA
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46
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Lee SJ, Hyun S, Kieft JS, Yu J. An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets. J Am Chem Soc 2009; 131:2224-30. [PMID: 19199621 DOI: 10.1021/ja807609m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hairpin RNA motif is one of the most frequently observed secondary structures and is often targeted by therapeutic agents. An amphiphilic peptide with seven lysine and eight leucine residues and its derivatives were designed for use as ligands against RNA hairpin motifs. We hypothesized that variations in both the hydrophobic leucine-rich and hydrophilic lysine-rich spheres of these amphiphilic peptides would create extra attractive interactions with hairpin RNA targets. A series of alanine-scanned peptides were probed to identify the most influential lysine residues in the hydrophilic sphere. The binding affinities of these modified peptides with several hairpins, such as RRE, TAR from HIV, a short hairpin from IRES of HCV, and a hairpin from the 16S A-site stem from rRNA, were determined. Since the hairpin from IRES of HCV was the most susceptible to the initial series of alanine-scanned peptides, studies investigating how further variations in the peptides effect binding employed the IRES hairpin. Next, the important Lys residues were substituted by shorter chain amines, such as ornithine, to place the peptide deeper into the hairpin groove. In a few cases, a 70-fold improved binding was observed for peptides that contained the specifically located shorter amine side chains. To further explore changes in binding affinities brought about by alterations in the hydrophobic sphere, tryptophan residues were introduced in place of leucine. A few peptides with tryptophan in specific positions also displayed 70-fold improved binding affinities. Finally, double mutant peptides incorporating both specifically located shorter amine side chains in the hydrophilic region and tryptophan residues in the hydrophobic region were synthesized. The binding affinities of peptides containing the simple double modification were observed to be 80 times lower, and their binding specificities were increased 40-fold. The results of this effort provide important information about strategies that can be used to prepare peptides that both strongly and selectively target hairpin RNAs. Specifically, the findings indicate that tailor-made amphiphilic peptide ligands against certain hairpin RNAs can be obtained if the RNA target possesses a deep groove in which both the hydrophobic and hydrophilic spheres of the peptide interact.
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Affiliation(s)
- Su Jin Lee
- Department of Chemistry and Education, Seoul National University, Seoul 151-748, Korea
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47
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Abstract
The enzymatic incorporation of a series of emissive pyrimidine analogues into RNA oligonucleotides is explored. T7 RNA polymerase is challenged with accepting three non-natural, yet related, triphosphates as substrates and incorporating them into diverse RNA transcripts. The three ribonucleoside triphosphates differ only in the modification of their uracil nucleus and include a thieno[3,2-d]pyrimidine nucleoside, a thieno[3,4-d]pyrimidine derivative, and a uridine containing a thiophene ring conjugated at its 5-position. All thiophene-containing uridine triphosphates (UTPs) get incorporated into RNA oligonucleotides at positions that are remote to the promoter, although the yields of the transcripts vary compared with the transcript obtained with only native triphosphates. Among the three derivatives, the 5-modified UTP is found to be the most "polymerase-friendly" and is well accommodated by T7 RNA polymerase. Although the fused thiophene analogues cannot be incorporated next to the promoter region, the 5-modified non-natural UTP gets incorporated near the promoter (albeit in relatively low yields) and even in multiple copies. Labeling experiments shed light on the mediocre incorporation of the fused analogues, suggesting the enzyme frequently pauses at the incorporation position. When incorporation does take place, the enzyme fails to elongate the modified oligonucleotide and yields aborted transcripts. Taken together, these results highlight the versatility and robustness, as well as the scope and limitation, of T7 RNA polymerase in accepting and incorporating reporter nucleotides into modified RNA transcripts.
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Affiliation(s)
- Seergazhi G Srivatsan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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Heterocyclic compounds that inhibit Rev-RRE function and human immunodeficiency virus type 1 replication. Antimicrob Agents Chemother 2008; 52:3169-79. [PMID: 18625767 DOI: 10.1128/aac.00274-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A cell-based screening assay was performed to identify compounds that inhibited the postintegration stage of the human immunodeficiency virus (HIV) life cycle. This assay utilized a cell line that contains the HIV gag and pol genes expressed in a Rev-dependent fashion. The cell line produces about 10 to 15 ng of p24 per milliliter of medium over a 24-h period in the form of viruslike particles. Any compound that inhibits a postintegration step in the HIV life cycle scores in this assay by decreasing particle production. Forty thousand compounds were screened, and 192 compounds were selected from the original screen because they showed more than 50% inhibition at a 10 muM concentration. The cumulative evidence presented in this study strongly suggests that 2 of the 192 compounds work as inhibitors of HIV Rev function. This was determined by a variety of cell-based assays, although the compounds do not interfere with Rev-RRE (Rev response element) binding in vitro. Both compounds inhibit replication of the lab isolate NL4-3 as well as an HIV primary isolate from Brazil (93BR021) and thus are promising leads as therapeutic candidates that target HIV replication through inhibition of Rev function.
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49
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Study on molecular interactions between proteins on live cell membranes using quantum dot-based fluorescence resonance energy transfer. Anal Bioanal Chem 2008; 391:2819-24. [DOI: 10.1007/s00216-008-2189-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 05/11/2008] [Accepted: 05/14/2008] [Indexed: 10/22/2022]
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50
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Affiliation(s)
- Jason R Thomas
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61822, USA
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