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Jyoti Maiti N, Ganguly S, Choowongkomon K, Seetaha S, Saehlee S, Aiebchun T. Synthesis, in vitro Anti-HIV-1RT evaluation, molecular modeling, DFT and acute oral toxicity studies of some benzotriazole derivatives. J Struct Biol 2024; 216:108094. [PMID: 38653343 DOI: 10.1016/j.jsb.2024.108094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 04/25/2024]
Abstract
This study synthesized and evaluated a series of benzotriazole derivatives denoted 3(a-j) and 6(a-j) for their anti-HIV-1 RT activities compared to the standard drug efavirenz. Notably, compound 3 h, followed closely by 6 h, exhibited significant anti-HIV-1 RT efficacy relative to the standard drug. In vivo oral toxicity studies were conducted for the most active compound 3 h, confirming its nontoxic nature to ascertain the safety profile. By employing molecular docking techniques, we explored the potential interactions between the synthesized compounds (ligands) and a target biomolecule (protein)(PDB ID 1RT2) at the molecular level. We undertook the molecular dynamics study of 3 h, the most active compound, within the active binding pocket of the cocrystallized structure of HIV-1 RT (PDB ID 1RT2). We aimed to learn more about how biomolecular systems behave, interact, and change at the atomic or molecular level over time. Finally, the DFT-derived HOMO and LUMO orbitals, as well as analysis of the molecular electrostatic potential map, aid in discerning the reactivity characteristics of our molecule.
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Affiliation(s)
- Nigam Jyoti Maiti
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Swastika Ganguly
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India.
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand.
| | - Supaphorn Seetaha
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand
| | - Siriwan Saehlee
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand
| | - Thitinan Aiebchun
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Pahon - Yothin Road, Chatuchak, Bangkok 10900, Thailand
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2
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Seetaha S, Kamonsutthipaijit N, Yagi-Utsumi M, Seako Y, Yamaguchi T, Hannongbua S, Kato K, Choowongkomon K. Biophysical Characterization of p51 and p66 Monomers of HIV-1 Reverse Transcriptase with Their Inhibitors. Protein J 2023; 42:741-752. [PMID: 37728788 DOI: 10.1007/s10930-023-10156-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2023] [Indexed: 09/21/2023]
Abstract
Human immunodeficiency virus (HIV)-1 reverse transcriptase (HIV-1 RT) is responsible for the transcription of viral RNA genomes into DNA genomes and has become an important target for the treatment of acquired immune deficiency syndrome (AIDS). This study used biophysical techniques to characterize the HIV-1 RT structure, monomer forms, and the non-nucleoside reverse transcriptase inhibitors (NNRTIs) bound forms. Inactive p66W401A and p51W401A were selected as models to study the HIV-1 RT monomer structures. Nuclear magnetic resonance (NMR) spectroscopy revealed that the unliganded forms of p66W401A protein and p51W401A protein had similar conformation to each other in solution. The complexes of p66W401A or p51W401A with inhibitors showed similar conformations to p66 in the RT heterodimer bound to the NNRTIs. Furthermore, the results of paramagnetic relaxation enhancement (PRE)-assisted NMR revealed that the unliganded forms of the p66W401A and p51W401A conformations were different from the unliganded heterodimer, characterized by a greater distance between the fingers and thumb subdomains. Small-angle X-ray scattering (SAXS) experiments confirmed that p66W401A and p51W401A can bind with inhibitors, similar to the p66/p51 heterodimer. The findings of this study increase the structural knowledge base of HIV-1 RT monomers, which may be helpful in the future design of potent viral inhibitors.
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Affiliation(s)
- Supaphorn Seetaha
- KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Nuntaporn Kamonsutthipaijit
- Synchrotron Light Research Institute, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Yanaka Seako
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Takumi Yamaguchi
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, Okazaki, Aichi, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Kiattawee Choowongkomon
- KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand.
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.
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3
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Sananboonudom S, Kaewnoi A, Pompimon W, Narakaew S, Jiajaroen S, Chainok K, Nuntasaen N, Suksen K, Chairoungdua A, Limthongkul J, Naparswad C, Pikulthong S, Meepowpan P, Wingwon B, Charoenphakinrattana N, Udomputtimekakul P. Study on the absolute configuration and biological activity of rotenoids from the leaves and twigs of Millettia pyrrhocarpa Mattapha, Forest & Hawkins, sp. Nov. BMC Complement Med Ther 2023; 23:147. [PMID: 37143007 PMCID: PMC10161675 DOI: 10.1186/s12906-023-03963-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND M. pyrrhocarpa is a new plant in the Fabaceae: Faboideae family that is found in Thailand. A literature search revealed that the Milletia genus is rich in bioactive compounds possessing a wide range of biological activities. In this study, we aimed to isolate novel bioactive compounds and to study their bioactivities. METHODS The hexane, ethyl acetate, and methanol extracts from the leaves and twigs of M. pyrrhocarpa were isolated and purified using chromatography techniques. These extracts and pure compounds were tested in vitro for their inhibitory activities against nine strains of bacteria, as well as their anti-HIV-1 virus activity and cytotoxicity against eight cancer cell lines. RESULTS Three rotenoids, named 6aS, 12aS, 12S-elliptinol (1), 6aS, 12aS, 12S-munduserol (2), dehydromunduserone (3), and crude extracts were evaluated for antibacterial, anti-HIV, and cytotoxic activities. It was found that compounds 1-3 inhibited the growth of nine strains of bacteria, and the best MIC/MBC values were obtained at 3/ > 3 mg/mL. The hexane extract showed anti-HIV-1 RT with the highest %inhibition at 81.27 at 200 mg/mL, while 6aS, 12aS, 12S-elliptinol (1) reduced syncytium formation in 1A2 cells with a maximum EC50 value of 4.48 μM. Furthermore, 6aS, 12aS, 12S-elliptinol (1) showed cytotoxicity against A549 and Hep G2 cells with maximum ED50 values of 2.27 and 3.94 μg/mL. CONCLUSION This study led to the isolation of constituents with potential for medicinal application, providing compounds (1-3) as lead compounds against nine strains of bacteria. The hexane extract showed the highest %inhibition of HIV-1 virus, Compound 1 showed the best EC50 in reducing syncytium formation in 1A2 cells, and it also showed the best ED50 against human lung adenocarcinoma (A549) and human hepatocellular carcinoma (Hep G2). The isolated compounds from M. pyrrhocarpa offered significant potential for future medicinal application studies.
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Affiliation(s)
- Suda Sananboonudom
- Department of Chemistry, Faculty of Science and Center of Innovation in Chemistry, Lampang Rajabhat University, Lampang, 52100, Thailand
| | - Atchara Kaewnoi
- Department of Thai Traditionnal Medicine, Faculty of Science and Technology, Bansomdejchaopraya Rajabhat University, Bangkok, 10600, Thailand
| | - Wilart Pompimon
- Department of Chemistry, Faculty of Science and Center of Innovation in Chemistry, Lampang Rajabhat University, Lampang, 52100, Thailand
| | - Samroeng Narakaew
- Department of Chemistry, Faculty of Science and Center of Innovation in Chemistry, Lampang Rajabhat University, Lampang, 52100, Thailand
| | - Suwadee Jiajaroen
- Thammasat University Research Unit in Multifunctional Crystalline Materials and Applications (TUMcMa), Faculty of Science and Technology, Thammasat University, Pathum Thani, 12121, Thailand
| | - Kittipong Chainok
- Thammasat University Research Unit in Multifunctional Crystalline Materials and Applications (TUMcMa), Faculty of Science and Technology, Thammasat University, Pathum Thani, 12121, Thailand
| | - Narong Nuntasaen
- Department of Chemistry, Faculty of Science and Center of Innovation in Chemistry, Mahidol University, Bangkok, 10400, Thailand
| | - Kanoknetr Suksen
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, 10600, Thailand
| | - Arthit Chairoungdua
- Department of Physiology, Faculty of Science, Mahidol University, Bangkok, 10600, Thailand
- Excellent Center for Drug Discovery (ECDD), Mahidol University, Bangkok, 10600, Thailand
- Toxicology Graduate Program, Faculty of Science, Mahidol University, Bangkok, 10600, Thailand
| | - Jitra Limthongkul
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10600, Thailand
| | - Chanita Naparswad
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10600, Thailand
| | - Suttiporn Pikulthong
- Department of Chemistry, Faculty of Science, Mahidol University, Bangkok, 10600, Thailand
| | - Puttinan Meepowpan
- Department of Chemistry, and Center for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50300, Thailand
| | - Boonthawan Wingwon
- Department of Management Science, Faculty of Management Science, Lampang Rajabhat University, Lampang, 52100, Thailand
| | | | - Phansuang Udomputtimekakul
- Department of Chemistry, Faculty of Science and Center of Innovation in Chemistry, Lampang Rajabhat University, Lampang, 52100, Thailand.
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4
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Udomputtimekakul P, Pompimon W, Chainok K, Jiajaroen S, Meepowpan P, Tata S, Tasit P, Rithchumpon P, Nuntasaen N. Krabasinolide A with anti-HIVs activity from the leaves and twigs of Croton krabas. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2022; 24:761-768. [PMID: 34592877 DOI: 10.1080/10286020.2021.1972979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 08/10/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
One new clerodane-type diterpenoid, together with one known, was isolated from the leaves and twigs of C. krabas. The structures of these compounds were elucidated as krabasinolide A (1) and taraxerol (2) by spectroscopic methods (UV, IR, HRESIMS, 1 D, and 2 D NMR), and the relative stereochemistry was confirmed by X-ray diffraction analysis with graphite monochromated Mo-Kα (λ = 0.71073 Å) radiation at 296(2) K. Extracts and compounds 1-2 were evaluated for in vitro antiviral activity.
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Affiliation(s)
- Phansuang Udomputtimekakul
- Laboratory of Natural Products, Center of Excellence for Innovation in Chemistry, Faculty of Science, Lampang Rajabhat University, Lampang 52100, Thailand
| | - Wilart Pompimon
- Laboratory of Natural Products, Center of Excellence for Innovation in Chemistry, Faculty of Science, Lampang Rajabhat University, Lampang 52100, Thailand
| | - Kittipong Chainok
- Materials and Textile Technology, Faculty of Science and Technology, Thammasat University, Pathum Thani 12121, Thailand
| | - Suwadee Jiajaroen
- Division of Chemistry, Faculty of Science and Technology, Thammasat University, Pathum Thani 12121, Thailand
| | - Puttinan Meepowpan
- Department of Chemistry, and Center for Innovation in Chemistry, Faculty of Science, Chiang Mai 50300 University, Chiang Mai, Thailand
| | - Saranchana Tata
- Laboratory of Natural Products, Center of Excellence for Innovation in Chemistry, Faculty of Science, Lampang Rajabhat University, Lampang 52100, Thailand
| | - Phatra Tasit
- Laboratory of Natural Products, Center of Excellence for Innovation in Chemistry, Faculty of Science, Lampang Rajabhat University, Lampang 52100, Thailand
| | - Puracheth Rithchumpon
- Department of Chemistry, and Center for Innovation in Chemistry, Faculty of Science, Chiang Mai 50300 University, Chiang Mai, Thailand
| | - Narong Nuntasaen
- The Forest Herbarium, Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand
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Biophysical Characterization of Novel DNA Aptamers against K103N/Y181C Double Mutant HIV-1 Reverse Transcriptase. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27010285. [PMID: 35011517 PMCID: PMC8746315 DOI: 10.3390/molecules27010285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 02/07/2023]
Abstract
The human immunodeficiency virus type-1 Reverse Transcriptase (HIV-1 RT) plays a pivotal role in essential viral replication and is the main target for antiviral therapy. The anti-HIV-1 RT drugs address resistance-associated mutations. This research focused on isolating the potential specific DNA aptamers against K103N/Y181C double mutant HIV-1 RT. Five DNA aptamers showed low IC50 values against both the KY-mutant HIV-1 RT and wildtype (WT) HIV-1 RT. The kinetic binding affinity forms surface plasmon resonance of both KY-mutant and WT HIV-1 RTs in the range of 0.06–2 μM and 0.15–2 μM, respectively. Among these aptamers, the KY44 aptamer was chosen to study the interaction of HIV-1 RTs-DNA aptamer complex by NMR experiments. The NMR results indicate that the aptamer could interact with both WT and KY-mutant HIV-1 RT at the NNRTI drug binding pocket by inducing a chemical shift at methionine residues. Furthermore, KY44 could inhibit pseudo-HIV particle infection in HEK293 cells with nearly 80% inhibition and showed low cytotoxicity on HEK293 cells. These together indicated that the KY44 aptamer could be a potential inhibitor of both WT and KY-mutant HIV-RT.
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6
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Tabassum T, Azeem SM, Muwonge AN, Frey KM. Application of Structure-based Methods to Analyze Resistance Mutations for Chemically Diverse Non-Nucleoside Reverse Transcriptase Inhibitors. Curr HIV Res 2021; 18:283-291. [PMID: 32493197 DOI: 10.2174/1570162x18666200603141209] [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: 12/18/2019] [Revised: 04/17/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are used in combination with antiretroviral therapy to suppress viral loads in HIV patients. The chemical design of NNRTIs has changed in recent years in response to resistance-associated mutations (RAMs) and resistance. NNRTIs are chemically diverse compounds that bind an allosteric site of HIV RT. Resistance- associated mutations (RAMs) identified in HIV patients are associated with NNRTI resistance. RAMs confer amino acid changes that alter both structural and physiochemical properties of the allosteric site. Ultimately, these changes reduce NNRTI affinity. Previously, we used a combination of computational and experimental methods to analyze and validate RAMs for 3 diarylpyrimidine (DAPY) NNRTIs. OBJECTIVE The objective of this study is to apply these methods to other chemically diverse, non- DAPY NNRTIs. MATERIALS AND METHODS We selected MIV-150 (experimental microbicide) and doravirine for this study. A computational and molecular modeling strategy was used to evaluate the effects of RAMs. Calculated changes in drug affinity and stability (ΔS + ΔA) were used to determine overall resistance levels: susceptible, low, intermediate, and high. The ΔS + ΔA values for K101P suggest that this mutation confers intermediate/high-level resistance to MIV-150, but remains susceptible to doravirine. Based on the determined resistance levels, we analyzed the models and used Molecular Dynamics (MD) to compare the interactions of MIV-150/doravirine with RT wild-type (WT) and RT (K101P). From MD, we found that key interactions were lost with RT (K101P), but were retained with doravirine. To experimentally validate our findings, we conducted a fluorescence-based reverse transcription assay for MIV-150 with RT (WT) and RT (K101P). IC50 values determined in assays showed a 101-fold change in potency for MIV-150, but essentially no change for doravirine. RESULTS Our computational and experimental results are also consistent with antiviral data reported in the literature. CONCLUSION We believe that this approach is effective for analyzing mutations to determine resistance profiles for chemically diverse NNRTIs in development.
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Affiliation(s)
- Tasnim Tabassum
- Long Island University, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, NY 11201, United States
| | - Syeda M Azeem
- Long Island University, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, NY 11201, United States
| | - Alecia N Muwonge
- Long Island University, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, NY 11201, United States
| | - Kathleen M Frey
- Fairleigh Dickinson University, School of Pharmacy and Health Sciences, Florham Park, NJ, United States
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7
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Ratanabunyong S, Aeksiri N, Yanaka S, Yagi-Utsumi M, Kato K, Choowongkomon K, Hannongbua S. Characterization of New DNA Aptamers for Anti-HIV-1 Reverse Transcriptase. Chembiochem 2020; 22:915-923. [PMID: 33095511 DOI: 10.1002/cbic.202000633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/22/2020] [Indexed: 11/09/2022]
Abstract
HIV-1 RT is a necessary enzyme for retroviral replication, which is the main target for antiviral therapy against AIDS. Effective anti-HIV-1 RT drugs are divided into two groups; nucleoside inhibitors (NRTI) and non-nucleoside inhibitors (NNRTI), which inhibit DNA polymerase. In this study, new DNA aptamers were isolated as anti-HIV-1 RT inhibitors. The selected DNA aptamer (WT62) presented with high affinity and inhibition against wild-type (WT) HIV-1 RT and gave a KD value of 75.10±0.29 nM and an IC50 value of 84.81±8.54 nM. Moreover, WT62 decreased the DNA polymerase function of K103 N/Y181 C double mutant (KY) HIV-1 RT by around 80 %. Furthermore, the ITC results showed that this aptamer has small binding enthalpies with both WT and KY HIV-1 RTs through which the complex might form a hydrophobic interaction or noncovalent bonding. The NMR result also suggested that the WT62 aptamer could bind with both WT and KY mutant HIV-1 RTs at the connection domain.
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Affiliation(s)
- Siriluk Ratanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Niran Aeksiri
- Department of Agricultural Sciences, Naresuan University, Phitsanlolok, 65000, Thailand
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and, Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, 12 Okazaki, Aichi, 444-8787, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and, Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, 12 Okazaki, Aichi, 444-8787, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and, Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, 12 Okazaki, Aichi, 444-8787, Japan
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand.,Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Bangkok, 10900, Thailand
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8
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Seetaha S, Ratanabunyong S, Tabtimmai L, Choowongkomon K, Rattanasrisomporn J, Choengpanya K. Anti-feline immunodeficiency virus reverse transcriptase properties of some medicinal and edible mushrooms. Vet World 2020; 13:1798-1806. [PMID: 33132590 PMCID: PMC7566271 DOI: 10.14202/vetworld.2020.1798-1806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/06/2020] [Indexed: 01/27/2023] Open
Abstract
Background and Aim Feline immunodeficiency virus (FIV) causes AIDS-like symptoms in domestic and wild cats. Treatment of infected cats has been performed using human anti-HIV drugs, which showed some limitations. This study aimed to determine the anti-FIV potential of some mushrooms. Materials and Methods A total of 17 medicinal and edible mushrooms were screened to find their inhibitory effect against FIV reverse transcriptase (FIV-RT). Three solvents, water, ethanol, and hexane, were used to prepare crude mushroom extracts. Fluorescence spectroscopy was used to perform relative inhibition and 50% inhibitory concentrations (IC50) studies. Results The ethanol extract from dried fruiting bodies of Inonotus obliquus showed the strongest inhibition with an IC50 value of 0.80±0.16 μg/mL. The hexane extract from dried mycelium of I. obliquus and ethanol and water extracts from fresh fruit bodies of Phellinus igniarius also exhibited strong activities with the IC50 values of 1.22±0.20, 4.33±0.39, and 6.24±1.42 μg/mL, respectively. The ethanol extract from fresh fruiting bodies of Cordyceps sinensis, hexane extracts from dried mycelium of I. obliquus, ethanol extracts of Ganoderma lucidum, hexane extracts of fresh fruiting bodies of Morchella esculenta, and fresh fruiting bodies of C. sinensis showed moderate anti-FIV-RT activities with IC50 values of 29.73±12.39, 49.97±11.86, 65.37±14.14, 77.59±8.31, and 81.41±17.10 μg/mL, respectively. These mushroom extracts show anti-FIV potential. Conclusion The extracts from I. obliquus, P. igniarius, C. sinensis, and M. esculenta showed potential anti-FIV activity.
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Affiliation(s)
- Supaphorn Seetaha
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand.,Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Siriluk Ratanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.,Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Lueacha Tabtimmai
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jatuporn Rattanasrisomporn
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand.,Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
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9
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Seetaha S, Hannongbua S, Rattanasrisomporn J, Choowongkomon K. Novel peptides with HIV-1 reverse transcriptase inhibitory activity derived from the fruits of Quercus infectoria. Chem Biol Drug Des 2020; 97:157-166. [PMID: 32757477 DOI: 10.1111/cbdd.13770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/28/2020] [Accepted: 07/25/2020] [Indexed: 01/07/2023]
Abstract
The HIV-1 reverse transcriptase (HIV-1 RT), which is responsible for transcription of viral RNA genomes into DNA genomes, has become an important target for the treatment of patients with HIV infection. Hydrolyzed peptides from plants are considered a new source of potential drugs. In order to develop new effective inhibitors, peptides extracted from 111 Asian medicinal plants were screened against the HIV-1 RT. The crude hydrolyzed peptides from the fruit peel of Quercus infectoria were selected for purification and peptide sequence determination by HPLC and LC-MS. Two peptides of interest were synthesized, and an IC50 test was performed to determine their ability to inhibit the HIV-1 RT. The IC50 values of the peptides AIHIILI and LIAVSTNIIFIVV were determined to be 274 ± 5.10 nm and 236.4 ± 7.07 nm, respectively. This indicated that these peptides could be further developed as potential HIV-1 RT inhibitors.
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Affiliation(s)
- Supaphorn Seetaha
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Jatuporn Rattanasrisomporn
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand.,Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok, Thailand
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10
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Thongphichai W, Tuchinda P, Pohmakotr M, Reutrakul V, Akkarawongsapat R, Napaswad C, Limthongkul J, Jenjittikul T, Saithong S. Anti-HIV-1 activities of constituents from the rhizomes of Boesenbergia thorelii. Fitoterapia 2019; 139:104388. [PMID: 31655087 DOI: 10.1016/j.fitote.2019.104388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/17/2019] [Accepted: 10/20/2019] [Indexed: 11/24/2022]
Abstract
A new lignan, thoreliin A (1), and a new bisnorlignan, thoreliin B (2), were isolated from a MeOH extract of the rhizomes of Boesenbergia thorelii. In addition, the known bisnorlignans 3 and 4, neolignan 5, phenylpropanoids 6-15, as well as benzenoids 18-21 were also obtained from the same source. The structures were elucidated based on their spectroscopic data. By single crystal X-ray analysis, the relative stereochemistry of 1 was confirmed. All isolated compounds were evaluated for anti-HIV-1 activities. Among them, thoreliin A (1) exhibited anti-HIV-1 activities on both HIV-1 reverse transcriptase (41.43% inhibition at 200 μg/mL) and syncytium reduction assays (EC50 20.6 μM, SI 3.7), while compounds 3-6, 9 and 11-21 showed anti-HIV-1 activity only in the anti-syncytium assay (EC50 6.6-454.1 μM, SI >1.32-7.75).
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Affiliation(s)
- Wisuwat Thongphichai
- Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Patoomratana Tuchinda
- Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Manat Pohmakotr
- Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Vichai Reutrakul
- Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Chanita Napaswad
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Jitra Limthongkul
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Thaya Jenjittikul
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Saowanit Saithong
- Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand; Medical Science Research and Innovation Institute, Prince of Songkla University, Songkhla 90112, Thailand
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11
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Structure-based methods to predict mutational resistance to diarylpyrimidine non-nucleoside reverse transcriptase inhibitors. J Mol Graph Model 2018; 79:133-139. [DOI: 10.1016/j.jmgm.2017.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 11/19/2022]
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12
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Okano H, Katano Y, Baba M, Fujiwara A, Hidese R, Fujiwara S, Yanagihara I, Hayashi T, Kojima K, Takita T, Yasukawa K. Enhanced detection of RNA by MMLV reverse transcriptase coupled with thermostable DNA polymerase and DNA/RNA helicase. Enzyme Microb Technol 2016; 96:111-120. [PMID: 27871370 DOI: 10.1016/j.enzmictec.2016.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 10/20/2022]
Abstract
Detection of mRNA is a valuable method for monitoring the specific gene expression. In this study, we devised a novel cDNA synthesis method using three enzymes, the genetically engineered thermostable variant of reverse transcriptase (RT), MM4 (E286R/E302K/L435R/D524A) from Moloney murine leukemia virus (MMLV), the genetically engineered variant of family A DNA polymerase with RT activity, K4polL329A from thermophilic Thermotoga petrophila K4, and the DNA/RNA helicase Tk-EshA from a hyperthermophilic archaeon Thermococcus kodakarensis. By optimizing assay conditions for three enzymes using Taguchi's method, 100 to 1000-fold higher sensitivity was achieved for cDNA synthesis than conventional assay condition using only RT. Our results suggest that DNA polymerase with RT activity and DNA/RNA helicase are useful to increase the sensitivity of cDNA synthesis.
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Affiliation(s)
- Hiroyuki Okano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuta Katano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ayako Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Ryota Hidese
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Tsukasa Hayashi
- Kainos Laboratories, Inc., 38-18, Hongo 2-chome, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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13
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Gray WT, Frey KM, Laskey SB, Mislak AC, Spasov KA, Lee WG, Bollini M, Siliciano RF, Jorgensen WL, Anderson KS. Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance. ACS Med Chem Lett 2015; 6:1075-9. [PMID: 26487915 DOI: 10.1021/acsmedchemlett.5b00254] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/31/2015] [Indexed: 11/29/2022] Open
Abstract
Catechol diether compounds have nanomolar antiviral and enzymatic activity against HIV with reverse transcriptase (RT) variants containing K101P, a mutation that confers high-level resistance to FDA-approved non-nucleoside inhibitors efavirenz and rilpivirine. Kinetic data suggests that RT (K101P) variants are as catalytically fit as wild-type and thus can potentially increase in the viral population as more antiviral regimens include efavirenz or rilpivirine. Comparison of wild-type structures and a new crystal structure of RT (K101P) in complex with a leading compound confirms that the K101P mutation is not a liability for the catechol diethers while suggesting that key interactions are lost with efavirenz and rilpivirine.
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Affiliation(s)
- William T. Gray
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Kathleen M. Frey
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Sarah B. Laskey
- Department
of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Andrea C. Mislak
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Krasimir A. Spasov
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Won-Gil Lee
- Department
of Chemistry, Yale University, New Haven, Connecticut 06530-8107, United States
| | - Mariela Bollini
- Department
of Chemistry, Yale University, New Haven, Connecticut 06530-8107, United States
| | - Robert F. Siliciano
- Department
of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06530-8107, United States
| | - Karen S. Anderson
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
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14
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Bahare RS, Ganguly S, Choowongkomon K, Seetaha S. Synthesis, HIV-1 RT inhibitory, antibacterial, antifungal and binding mode studies of some novel N-substituted 5-benzylidine-2,4-thiazolidinediones. ACTA ACUST UNITED AC 2015; 23:6. [PMID: 25617150 PMCID: PMC4308940 DOI: 10.1186/s40199-014-0086-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/20/2014] [Indexed: 12/02/2022]
Abstract
Background Structural modifications of thiazolidinediones at 3rd and 5th position have exhibited significant biological activities. In view of the facts, and based on in silico studies carried out on thiazolidine-2,4-diones as HIV-1- RT inhibitors, a novel series of 2,4-thiazolidinedione analogs have been designed and synthesized. Methods Title compounds were prepared by the reported method. Conformations of the structures were assigned on the basis of results of different spectral data. The assay of HIV-1 RT was done as reported by Silprasit et al. Antimicrobial activity was determined by two fold serial dilution method. Docking study was performed for the highest active compounds by using Glide 5.0. Results The newly synthesized compounds were evaluated for their HIV-1 RT inhibitory activity. Among the synthesized compounds, compound 24 showed significant HIV-1 RT inhibitory activity with 73% of inhibition with an IC50 value of 1.31 μM. Compound 10 showed highest activity against all the bacterial strains. A molecular modeling study was carried out in order to investigate the possible interactions of the highest active compounds 24, 10 and 4 with the non nucleoside inhibitory binding pocket(NNIBP) of RT, active site of GlcN-6-P synthase and cytochrome P450 14-α-sterol demethylase from Candida albicans (Candida P450DM) as the target receptors respectively using the Extra Precision (XP) mode of Glide software. Conclusion A series of novel substituted 2-(5-benzylidene-2,4-dioxothiazolidin-3-yl)-N-(phenyl)propanamides (4–31) have been synthesized and evaluated for their HIV-1 RT inhibitory activity, antibacterial and antifungal activities. Some of the compounds have shown significant activity. Molecular docking studies showed very good interaction.
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Affiliation(s)
- Radhe Shyam Bahare
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India.
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15
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Dineshkumar K, Aparna V, Madhuri KZ, Hopper W. Biological activity of sporolides A and B from Salinispora tropica: in silico target prediction using ligand-based pharmacophore mapping and in vitro activity validation on HIV-1 reverse transcriptase. Chem Biol Drug Des 2014; 83:350-61. [PMID: 24165098 DOI: 10.1111/cbdd.12252] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/09/2013] [Indexed: 11/29/2022]
Abstract
Sporolides A and B are novel polycyclic macrolides from the obligate marine actinomycetes, Salinispora tropica. The unique and novel structure of sporolides makes them interesting candidates for targeting diverse biological activities. Biological target prediction of sporolides was carried out using ligand-based pharmacophore screening against known inhibitors and drugs. Validation of pharmacophore screening was carried out for the identified hits. New biological targets predicted for sporolides using this method were HIV-1 reverse transcriptase, adenosine A3 receptor, endothelin receptor ET-A, oxytocin receptor, voltage-gated L-type calcium channel α-1C subunit/calcium channel α/Δ subunit 1. Drug-likeness properties were predicted for the selected compounds using QikProp module. Sporolides A and B showed maximum docking score with HIV-1 reverse transcriptase. Structural interaction fingerprints analysis indicated similar binding pattern of the sporolides with the HIV-1 reverse transcriptase. Sporolide B exhibited good inhibitory activity against HIV-1 reverse transcriptase in in vitro fluorescent assay.
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Affiliation(s)
- Kesavan Dineshkumar
- Department of Bioinformatics, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur, 603203, TamilNadu, India
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