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Shin YH, Kim DE, Yu KL, Park CM, Kim HG, Kim KC, Bae S, Yoon CH. A Novel Time-Resolved Fluorescence Resonance Energy Transfer Assay for the Discovery of Small-Molecule Inhibitors of HIV-1 Tat-Regulated Transcription. Int J Mol Sci 2023; 24:ijms24119139. [PMID: 37298089 DOI: 10.3390/ijms24119139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) transactivator (Tat)-mediated transcription is essential for HIV-1 replication. It is determined by the interaction between Tat and transactivation response (TAR) RNA, a highly conserved process representing a prominent therapeutic target against HIV-1 replication. However, owing to the limitations of current high-throughput screening (HTS) assays, no drug that disrupts the Tat-TAR RNA interaction has been uncovered yet. We designed a homogenous (mix-and-read) time-resolved fluorescence resonance energy transfer (TR-FRET) assay using europium cryptate as a fluorescence donor. It was optimized by evaluating different probing systems for Tat-derived peptides or TAR RNA. The specificity of the optimal assay was validated by mutants of the Tat-derived peptides and TAR RNA fragment, individually and by competitive inhibition with known TAR RNA-binding peptides. The assay generated a constant Tat-TAR RNA interaction signal, discriminating the compounds that disrupted the interaction. Combined with a functional assay, the TR-FRET assay identified two small molecules (460-G06 and 463-H08) capable of inhibiting Tat activity and HIV-1 infection from a large-scale compound library. The simplicity, ease of operation, and rapidity of our assay render it suitable for HTS to identify Tat-TAR RNA interaction inhibitors. The identified compounds may also act as potent molecular scaffolds for developing a new HIV-1 drug class.
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Affiliation(s)
- Young Hyun Shin
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Dong-Eun Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Kyung Lee Yu
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Chul Min Park
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Hong Gi Kim
- Department for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Daejeon 34114, Republic of Korea
| | - Kyung-Chang Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Songmee Bae
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, 187 Osongsaengmyeong 2-ro, Cheongju 363951, Republic of Korea
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Identification of 3-Oxindole Derivatives as Small Molecule HIV-1 Inhibitors Targeting Tat-Mediated Viral Transcription. Molecules 2022; 27:molecules27154921. [PMID: 35956872 PMCID: PMC9370035 DOI: 10.3390/molecules27154921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The heterocyclic indole structure has been shown to be one of the most promising scaffolds, offering various medicinal advantages from its wide range of biological activity. Nonetheless, the significance of 3-oxindole has been less known. In this study, a series of novel 3-oxindole-2-carboxylates were synthesized and their antiviral activity against human immunodeficiency virus-1 (HIV-1) infection was evaluated. Among these, methyl (E)-2-(3-chloroallyl)-4,6-dimethyl-one (6f) exhibited the most potent inhibitory effect on HIV-1 infection, with a half-maximal inhibitory concentration (IC50) of 0.4578 μM but without severe cytotoxicity (selectivity index (SI) = 111.37). The inhibitory effect of these compounds on HIV-1 infection was concordant with their inhibitory effect on the viral replication cycle. Mode-of-action studies have shown that these prominent derivatives specifically inhibited the Tat-mediated viral transcription on the HIV-1 LTR promoter instead of reverse transcription or integration. Overall, our findings indicate that 3-oxindole derivatives could be useful as a potent scaffold for the development of a new class of anti-HIV-1 agents.
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Shin YH, Park CM, Yoon CH. An Overview of Human Immunodeficiency Virus-1 Antiretroviral Drugs: General Principles and Current Status. Infect Chemother 2021; 53:29-45. [PMID: 34409780 PMCID: PMC8032919 DOI: 10.3947/ic.2020.0100] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
Treatment with highly active antiretroviral therapy (HAART) can prolong a patient's life-span by disrupting pivotal steps in the replication cycle of the human immunodeficiency virus-1 (HIV-1). However, drug resistance is emerging as a major problem worldwide due to the prolonged period of treatment undergone by HIV-1 patients. Since the approval of zidovudine in 1987, over thirty antiretroviral drugs have been categorized into the following six distinct classes based on their biological function and resistance profiles: (1) nucleoside analog reverse-transcriptase inhibitors; (2) non–nucleoside reverse transcriptase inhibitors; (3) integrase strand transferase inhibitors; (4) protease inhibitors; (5) fusion inhibitors; and (6) co-receptor antagonists. Additionally, several antiretroviral drugs have been developed recently, such as a long active drug, humanized antibody and pro-drug metabolized into an active form in the patient's body. Although plenty of antiretroviral drugs are beneficially used to treat patients with HIV-1, the ongoing efforts to develop antiretroviral drugs have overcome the drug resistances, adverse effects, and limited adherence of drugs observed in previous drugs to some extent. Furthermore, studies focused on agents targeting latent HIV-1 reservoirs should be strengthened, as that may lead to eradication of HIV-1.
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Affiliation(s)
- Young Hyun Shin
- Division of Chronic Viral Disease Research, Center for Emerging Virus Research, Korea National Institute of Health, Chungbuk, Korea
| | - Chul Min Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Korea
| | - Cheol Hee Yoon
- Division of Chronic Viral Disease Research, Center for Emerging Virus Research, Korea National Institute of Health, Chungbuk, Korea.
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Kelly ML, Chu CC, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA (NEW YORK, N.Y.) 2021; 27:12-26. [PMID: 33028652 PMCID: PMC7749633 DOI: 10.1261/rna.076257.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/26/2020] [Indexed: 05/30/2023]
Abstract
Identifying small molecules that selectively bind an RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to nonspecific binding of aminoglycosides and intercalators to many stem-loop RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities. However, target engagement and cellular selectivity assays are not routinely performed, and it is often unclear whether functional activity directly results from specific binding to the target RNA. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activities of distinct stem-loop RNAs, to bind and inhibit the cellular activities of two unrelated HIV-1 stem-loop RNAs: the transactivation response element (TAR) and the rev response element stem IIB (RREIIB). All compounds bound TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting off-target interactions consistent with nonspecific activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that aminoglycosides and drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, in contrast to ligands that specifically bind riboswitches. Our results demonstrate that drug-like molecules can nonspecifically bind stem-loop RNAs most likely through hydrogen bonding and electrostatic interactions and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.
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Affiliation(s)
- Megan L Kelly
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chia-Chieh Chu
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Honglue Shi
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Laura R Ganser
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hal P Bogerd
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Kelly Huynh
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yuze Hou
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Shin Y, Park CM, Kim HG, Kim DE, Choi MS, Kim JA, Choi BS, Yoon CH. Identification of Aristolactam Derivatives That Act as Inhibitors of Human Immunodeficiency Virus Type 1 Infection and Replication by Targeting Tat-Mediated Viral Transcription. Virol Sin 2020; 36:254-263. [PMID: 32779073 DOI: 10.1007/s12250-020-00274-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/28/2020] [Indexed: 11/26/2022] Open
Abstract
Despite the success of antiretroviral therapy (ART), efforts to develop new classes of antiviral agents have been hampered by the emergence of drug resistance. Dibenzo-indole-bearing aristolactams are compounds that have been isolated from various plants species and which show several clinically relevant effects, including anti-inflammatory, antiplatelet, and anti-mycobacterial actions. However, the effect of these compounds on human immunodeficiency virus type 1 (HIV-1) infection has not yet been studied. In this study, we discovered an aristolactam derivative bearing dibenzo[cd,f]indol-4(5H)-one that had a potent anti-HIV-1 effect. A structure-activity relationship (SAR) study using nine synthetic derivatives of aristolactam identified the differing effects of residue substitutions on the inhibition of HIV-1 infection and cell viability. Among the compounds tested, 1,2,8,9-tetramethoxy-5-(2-(piperidin-1-yl)ethyl)-dibenzo[cd,f]indol-4(5H)-one (Compound 2) exhibited the most potent activity by inhibiting HIV-1 infection with a half-maximal inhibitory concentration (IC50) of 1.03 μmol/L and a half-maximal cytotoxic concentration (CC50) of 16.91 μmol/L (selectivity index, 16.45). The inhibitory effect of the compounds on HIV-1 infection was linked to inhibition of the viral replication cycle. Mode-of-action studies showed that the aristolactam derivatives did not affect reverse transcription or integration; instead, they specifically inhibited Tat-mediated viral transcription. Taken together, these findings show that several aristolactam derivatives impaired HIV-1 infection by inhibiting the activity of Tat-mediated viral transcription, and suggest that these derivatives could be antiviral drug candidates.
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Affiliation(s)
- YoungHyun Shin
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Heungdeok-gu, Cheongju-si, Chungbuk, 28159, Republic of Korea
| | - Chul Min Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Hong Gi Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Dong-Eun Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Heungdeok-gu, Cheongju-si, Chungbuk, 28159, Republic of Korea
| | - Min Suk Choi
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Jeong-Ah Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Heungdeok-gu, Cheongju-si, Chungbuk, 28159, Republic of Korea
| | - Byeong-Sun Choi
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Heungdeok-gu, Cheongju-si, Chungbuk, 28159, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Heungdeok-gu, Cheongju-si, Chungbuk, 28159, Republic of Korea.
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Shin Y, Kim HG, Park CM, Choi MS, Kim DE, Choi BS, Kim K, Yoon CH. Identification of novel compounds against Tat-mediated human immunodeficiency virus-1 transcription by high-throughput functional screening assay. Biochem Biophys Res Commun 2019; 523:368-374. [PMID: 31866007 DOI: 10.1016/j.bbrc.2019.12.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
Abstract
Trans-activator (Tat)-mediated human immunodeficiency virus type 1 (HIV-1) transcription is essential for the replication of HIV-1 and is considered a potent therapeutic target for HIV-1 inhibition. In this study, the Library of Pharmacologically Active Compounds (LOPAC1280) was screened using our dual-reporter screening system for repositioning as Tat-inhibitory compounds. Consequently, two compounds were found to be potent, with low cytotoxicity. Of these two compounds, Roscovitine (CYC202) is already known to be a Tat inhibitor, while gemcitabine has been newly identified as an inhibitor of Tat-mediated transcription linked to viral production and replication. In an additional screening using the ribonucleoside analogues of gemcitabine, two analogues (2'-C-methylcytidine and 3-deazauridine) showed a specific Tat-inhibitory effect linked to their anti-HIV-1 activity. Interestingly, these compounds did not affect Tat protein directly, while the mechanism underlying their inhibition of Tat-mediated transcription was linked to pyrimidine biosynthesis, rather than to alteration of the dNTP pool, influenced by the inhibition of ribonucleotide reductase. Taken together, the proposed functional screening system is a useful tool for the identification of inhibitors of Tat-mediated HIV-1 transcription from among a large number of compounds, and the inhibitory effect of HIV-1 transcription by gemcitabine and its analogues may suggest a strategy for developing a new class of therapeutic anti-HIV drugs.
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Affiliation(s)
- YoungHyun Shin
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea
| | - Hong Gi Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Chul Min Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Min Suk Choi
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Dong-Eun Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea
| | - Byeong-Sun Choi
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea
| | - Kisoon Kim
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Viral Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Chungbuk, Republic of Korea.
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Kang K, Huang L, Li Q, Liao X, Dang Q, Yang Y, Luo J, Zeng Y, Li L, Gou D. An improved Tet-on system in microRNA overexpression and CRISPR/Cas9-mediated gene editing. J Anim Sci Biotechnol 2019; 10:43. [PMID: 31198556 PMCID: PMC6556963 DOI: 10.1186/s40104-019-0354-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/12/2019] [Indexed: 11/10/2022] Open
Abstract
Background Tetracycline (Tet)-regulated expression system has become a widely applied tool to control gene activity. This study aimed to improve the Tet-on system with superior regulatory characteristics. Results By comprehensively comparing factors of transactivators, Tet-responsive elements (TREs), orientations of induced expression cassette, and promoters controlling the transactivator, we developed an optimal Tet-on system with enhanced inducible efficiency and lower leakiness. With the system, we successfully performed effective inducible and reversible expression of microRNA, and presented a more precise and easily reproducible fine-tuning for confirming the target of a miRNA. Finally, the system was applied in CRISPR/Cas9-mediated knockout of nuclear factor of activated T cells-5 (NFAT5), a protective transcription factor in cellular osmoregulation. Conclusions This study established an improved Tet-on system for powerful and stringent gene regulation in functional genetic studies. Electronic supplementary material The online version of this article (10.1186/s40104-019-0354-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kang Kang
- 1Department of Biochemistry and Molecular Biology, Carson International Cancer Center, Shenzhen University Health Sciences Center, Shenzhen, Guangdong 518060 People's Republic of China
| | - Lian Huang
- 2Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 People's Republic of China
| | - Qing Li
- 3Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Xueyuan Ave 1066, Shenzhen, Guangdong 518060 People's Republic of China
| | - Xiaoyun Liao
- 3Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Xueyuan Ave 1066, Shenzhen, Guangdong 518060 People's Republic of China
| | - Quanjin Dang
- 3Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Xueyuan Ave 1066, Shenzhen, Guangdong 518060 People's Republic of China
| | - Yi Yang
- 1Department of Biochemistry and Molecular Biology, Carson International Cancer Center, Shenzhen University Health Sciences Center, Shenzhen, Guangdong 518060 People's Republic of China
| | - Jun Luo
- 2Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 People's Republic of China
| | - Yan Zeng
- 3Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Xueyuan Ave 1066, Shenzhen, Guangdong 518060 People's Republic of China
| | - Li Li
- 3Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Xueyuan Ave 1066, Shenzhen, Guangdong 518060 People's Republic of China
| | - Deming Gou
- 1Department of Biochemistry and Molecular Biology, Carson International Cancer Center, Shenzhen University Health Sciences Center, Shenzhen, Guangdong 518060 People's Republic of China.,3Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Xueyuan Ave 1066, Shenzhen, Guangdong 518060 People's Republic of China
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