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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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Singh A, Kumar V, Mishra A, Singh VK. Targeting the HIV-1 Tat and Human Tat Protein Complex through Natural
Products: An In Silico Docking and Molecular Dynamics Simulation
Approach. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220330122542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Tat protein is considered essential for substantial HIV-1 replication, and is also
required to break HIV-1 latency, resulting in productive HIV replication. The multifaceted regulatory role
of HIV Tat and the fact that it is expressed in the early stages of HIV infection justify its potential as an
anti-HIV drug target.
Objective:
The present study was undertaken with the aim to target HIV-1 Tat protein with natural compounds
which could help in identifying potential inhibitors against HIV-1 Tat.
Methods:
In this study, we compared the binding of Tat protein and Human P-TEFb Tat protein complex
(TPC) with phyto-steroids and terpenes to evaluate their potential for HIV-1 treatment. The docking ability
of plant products with HIV-1 Tat and TPC was studied with respect to dissociation constant, geometric
shape complementary score, approximate interface area, and binding energy using Patch dock and
YASARA. Molecular dynamics simulation was set up to investigate the interactions of the natural compounds
with Tat protein and human tat protein complex (TPC).
Results:
The binding energy and dissociation constant of Diosgenin, Catharanthine and Ginkgolide A
with Tat and TPC were comparable to antiretroviral drugs, Maraviroc and Emtricitabine. The natural
products, Diosgenin, Ginkgolide A and Catharanthine, showed the highest binding energy and were stable
with Tat protein and TPC in the entire MD simulation run.
Conclusion:
The natural products, Diosgenin, Ginkgolide A and Catharanthine, showed highest binding
energy and were stable with Tat protein and TPC in the entire MD simulation run. The binding energy
and dissociation constant of Diosgenin, Catharanthine and Ginkgolide A with Tat and TPC were comparable
to antiretroviral drugs, Maraviroc and Emtricitabine.
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Affiliation(s)
- Anchal Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Vipin Kumar
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Ayushi Mishra
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Vinay Kumar Singh
- Centre for
Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, U.P., India
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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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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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Modeling of the HIV-1 Life Cycle in Productively Infected Cells to Predict Novel Therapeutic Targets. Pathogens 2020; 9:pathogens9040255. [PMID: 32244421 PMCID: PMC7238236 DOI: 10.3390/pathogens9040255] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
There are many studies that model the within-host population dynamics of Human Immunodeficiency Virus Type 1 (HIV-1) infection. However, the within-infected-cell replication of HIV-1 remains to be not comprehensively addressed. There exist rather few quantitative models describing the regulation of the HIV-1 life cycle at the intracellular level. In treatment of HIV-1 infection, there remain issues related to side-effects and drug-resistance that require further search "...for new and better drugs, ideally targeting multiple independent steps in the HIV-1 replication cycle" (as highlighted recently by Teldury et al., The Future of HIV-1 Therapeutics, 2015). High-resolution mathematical models of HIV-1 growth in infected cells provide an additional analytical tool in identifying novel drug targets. We formulate a high-dimensional model describing the biochemical reactions underlying the replication of HIV-1 in target cells. The model considers a nonlinear regulation of the transcription of HIV-1 mediated by Tat and the Rev-dependent transport of fully spliced and singly spliced transcripts from the nucleus to the cytoplasm. The model is calibrated using available information on the kinetics of various stages of HIV-1 replication. The sensitivity analysis of the model is performed to rank the biochemical processes of HIV-1 replication with respect to their impact on the net production of virions by one actively infected cell. The ranking of the sensitivity factors provides a quantitative basis for identifying novel targets for antiviral therapy. Our analysis suggests that HIV-1 assembly depending on Gag and Tat-Rev regulation of transcription and mRNA distribution present two most critical stages in HIV-1 replication that can be targeted to effectively control virus production. These processes are not covered by current antiretroviral treatments.
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