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Nguyen HB, Nguyen CT, Pham MQ, Hoang L, Sansone A, Jannini EA. Perceived intravaginal ejaculation latency time: The diagnosis of premature ejaculation among Vietnamese men. Andrology 2024; 12:618-623. [PMID: 37615496 DOI: 10.1111/andr.13516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023]
Abstract
INTRODUCTION Premature ejaculation (PE) is a prevalent sexual dysfunction in men that greatly affects their quality of life. In PE, the duration of sexual performance is considered an important aspect. However, a self-estimated value of intravaginal ejaculation latency time (perceived IELT, PIELT) as a criterion for diagnosis has not been specified. AIM This study aimed to determine the validity and a threshold value for PIELT in PE diagnosis. METHOD In our cross-sectional study, we recruited 550 men from March 2019 to January 2020 and interviewed them regarding their general demographic characteristics, sexual habits, PIELT and completed a premature ejaculation diagnostic tool (PEDT) questionnaire. Eventually, a combination of a clinical diagnosis and PEDT score was used, in which those with PEDT ≥ 11 and diagnosed with possible PE were assigned to the final PE(+) group; those with PEDT score ≤ 8 and diagnosed with no PE were included in the final PE(-) group. RESULTS Men PE(-) had more frequent sexual intercourse (9.74 ± 5.38 vs. 6.69 ± 5.38 episodes per month, p < 0.001) and had higher marriage rate (72.7% vs. 60.4%, p = 0.002) than PE(+) patients. No significant difference was noted regarding age, smoking habit, age of first sexual experience, and number of sexual partners between the two groups. The mean PIELT of control subjects and PE(+) patients were 11.69 ± 6.83 min and 2.01 ± 1.21 min, respectively. On receiver operating characteristic curve analysis, the cut-off value of PIELT of 3.75 min can be used to distinguish PE men (area under the curve = 0.982, sensitivity/specificity = 0.961/0.909), which means that men with a PIELT ≤ 3.5 min is suggestive of PE. CONCLUSION The impact of PE is dramatic both from a social and a personal perspective. PE(+) patients married significantly less and have significantly lower sexual activity compared to a PE(-) population. Furthermore, a PIELT of ≤ 3.5 min predicts PE demonstrating the need to revise its taxonomy and definition.
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Affiliation(s)
- Hoai Bac Nguyen
- Department of Andrology and Sexual Medicine, Hanoi Medical University's Hospital, Hanoi, Vietnam
| | - Cao Thang Nguyen
- Department of Andrology and Sexual Medicine, Hanoi Medical University's Hospital, Hanoi, Vietnam
| | - Minh Quan Pham
- Department of Andrology and Sexual Medicine, Hanoi Medical University's Hospital, Hanoi, Vietnam
| | - Long Hoang
- Department of Urology, Hanoi Medical University's Hospital, Hanoi, Vietnam
| | - Andrea Sansone
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Emmanuele A Jannini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Honorary Chair of Sexual Medicine, Hanoi Medical University, Hanoi, Vietnam
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Tam NM, Nguyen TH, Pham MQ, Hong ND, Tung NT, Vu VV, Quang DT, Ngo ST. Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations. J Mol Graph Model 2023; 124:108535. [PMID: 37295158 PMCID: PMC10233213 DOI: 10.1016/j.jmgm.2023.108535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The first oral drug for the treatment of COVID-19, Paxlovid, has been authorized; however, nirmatrelvir, a major component of the drug, is reported to be associated with some side effects. Moreover, the appearance of many novel variants raises concerns about drug resistance, and designing new potent inhibitors to prevent viral replication is thus urgent. In this context, using a hybrid approach combining machine learning (ML) and free energy simulations, 6 compounds obtained by modifying nirmatrelvir were proposed to bind strongly to SARS-CoV-2 Mpro. The structural modification of nirmatrelvir significantly enhances the electrostatic interaction free energy between the protein and ligand and slightly decreases the vdW term. However, the vdW term is the most important factor in controlling the ligand-binding affinity. In addition, the modified nirmatrelvir might be less toxic to the human body than the original inhibitor.
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Affiliation(s)
- Nguyen Minh Tam
- Faculty of Basic Sciences, University of Phan Thiet, Phan Thiet City, Binh Thuan, Viet Nam
| | - Trung Hai Nguyen
- Laboratory of Biophysics, Institute for Advanced Study in Technology, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Nam Dao Hong
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Nguyen Thanh Tung
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Viet Nam.
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Duong Tuan Quang
- Department of Chemistry, Hue University, Thua Thien Hue Province, Hue City, Viet Nam.
| | - Son Tung Ngo
- Laboratory of Biophysics, Institute for Advanced Study in Technology, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam.
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Le TTH, Tran LH, Nguyen MT, Pham MQ, Phung HTT. Calculation of binding affinity of JAK1 inhibitors via accurately computational estimation. J Biomol Struct Dyn 2023; 41:7224-7234. [PMID: 36069111 DOI: 10.1080/07391102.2022.2118830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Abstract
Janus kinase 1 (JAK1) is a tyrosine kinase that is involved in the initiation of responses to a number of different cytokine receptor families. The JAK1-dependent pathway is a therapeutic target, and several JAK inhibitors have been developed thanks to intensive research. However, since the ATP binding sites of JAK family members are quite alike, JAK1 inhibitors can thus be less selective, resulting in unanticipated adverse effects. Despite this, minor variations in the ATP-binding site have been extensively used to find a variety of small compounds with different inhibitory properties. Stronger binding affinity of JAK1 inhibitors is believed to be able to reduce the negative effects, leading to better treatment results. Therefore, a thorough computational search that can effectively identify ligands with extremely high binding affinity for JAK1 to serve as promising inhibitors is required. Here, a method combining steered-molecular dynamic (SMD) simulations with a modified linear interaction energy (LIE) model has been developed to evaluate the binding affinities of known JAK1 inhibitors. The correlation coefficient between the estimated and experimental values was 0.72 and a root-mean-square error was 0.97 kcal•mol-1, revealing that the SMD/LIE method can precisely and quickly predict the binding free energies of JAK1 inhibitors. Furthermore, three marine fungus-derived compounds, namely hansforesters E, hansforesters G and tetroazolemycins B, were identified to be particularly promising JAK1 inhibitors, accordingly. These findings show that the SMD/LIE method has a lot of promise for in silico screening of possible JAK1 inhibitors from a vast number of compounds that are now accessible.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thi-Thuy-Huong Le
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Linh Hoang Tran
- Vietnam National University, Ho Chi Minh City, Vietnam
- Faculty of Civil Engineering, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Vietnam
| | - Minh Tam Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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Tam NM, Tran LH, Vo QV, Pham MQ, Phung HTT. Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep-Learning and Steered-Molecular Dynamic Simulations. J Comput Biophys Chem 2023. [DOI: 10.1142/s2737416523500242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Nguyen TH, Thai QM, Pham MQ, Minh PTH, Phung HTT. Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds. Mol Divers 2023:10.1007/s11030-023-10601-1. [PMID: 36823394 PMCID: PMC9950021 DOI: 10.1007/s11030-023-10601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023]
Abstract
To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of SARS-CoV-2. In this study, we combined machine-learning (ML) model with atomistic simulations to computationally search for highly promising SARS-CoV-2 Mpro inhibitors from the representative natural compounds of the National Cancer Institute (NCI) Database. First, the trained ML model was used to scan the library quickly and reliably for possible Mpro inhibitors. The ML output was then confirmed using atomistic simulations integrating molecular docking and molecular dynamic simulations with the linear interaction energy scheme. The results turned out to show that there was evidently good agreement between ML and atomistic simulations. Ten substances were proposed to be able to inhibit SARS-CoV-2 Mpro. Seven of them have high-nanomolar affinity and are very potential inhibitors. The strategy has been proven to be reliable and appropriate for fast prediction of SARS-CoV-2 Mpro inhibitors, benefiting for new emerging SARS-CoV-2 variants in the future accordingly.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Quynh Mai Thai
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Thi Hong Minh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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Thuy HNT, Le AN, Pham MQ, Vo NB, Ngo QA. Multicomponent Synthesis of New 5‐thiourea‐4‐aza‐2,3 didehydropodophyllotoxins as Potent Cytotoxic Agents. J Heterocycl Chem 2023. [DOI: 10.1002/jhet.4633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- Hang Nguyen Thi Thuy
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Anh Nguyen Le
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry (INPC) , Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Graduate University of Science and Technology (GUST) , Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Ngoc Binh Vo
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Quoc Anh Ngo
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
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Yang SG, Nguyen HP, Hue BTB, Tran HP, Pham MQ, Quang De T, HIEU LETRONG, HONG QUANGVINH, NGUYEN CQCUONG, NGUYEN QUYPHU, Jung H, Yoo HJ. Novel Histone Deacetylase 6 Inhibitors Using Benzimidazole as Caps for Cancer Treatment. NEW J CHEM 2023. [DOI: 10.1039/d2nj05731j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Histone deacetylases (HDACs) have proven to be promising targets for the development of anticancer drugs. In this work, we report the design and synthesis of a series of 19 novel...
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Ngo ST, Nguyen TH, Tung NT, Vu VV, Pham MQ, Mai BK. Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches. Phys Chem Chem Phys 2022; 24:29266-29278. [PMID: 36449268 DOI: 10.1039/d2cp04476e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Computational approaches, including physics- and knowledge-based methods, have commonly been used to determine the ligand-binding affinity toward SARS-CoV-2 main protease (Mpro or 3CLpro). Strong binding ligands can thus be suggested as potential inhibitors for blocking the biological activity of the protease. In this context, this paper aims to provide a short review of computational approaches that have recently been applied in the search for inhibitor candidates of Mpro. In particular, molecular docking and molecular dynamics (MD) simulations are usually combined to predict the binding affinity of thousands of compounds. Quantitative structure-activity relationship (QSAR) is the least computationally demanding and therefore can be used for large chemical collections of ligands. However, its accuracy may not be high. Moreover, the quantum mechanics/molecular mechanics (QM/MM) method is most commonly used for covalently binding inhibitors, which also play an important role in inhibiting the activity of SARS-CoV-2. Furthermore, machine learning (ML) models can significantly increase the searching space of ligands with high accuracy for binding affinity prediction. Physical insights into the binding process can then be confirmed via physics-based calculations. Integration of ML models into computational chemistry provides many more benefits and can lead to new therapies sooner.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam. .,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam. .,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Ngo ST, Nguyen TH, Tung NT, Vue VV, Pham MQ, Mai BK. Correction: Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches. Phys Chem Chem Phys 2022; 25:878. [PMID: 36511167 DOI: 10.1039/d2cp90233h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Correction for 'Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches' by Son Tung Ngo et al., Phys. Chem. Chem. Phys., 2022, https://doi.org/10.1039/d2cp04476e.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam. .,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam. .,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Van V Vue
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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Pham MQ, Vu KB, Han Pham TN, Thuy Huong LT, Tran LH, Tung NT, Vu VV, Nguyen TH, Ngo ST. Correction: Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations. RSC Adv 2022; 12:35778. [PMID: 36545115 PMCID: PMC9751897 DOI: 10.1039/d2ra90114e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
[This corrects the article DOI: 10.1039/D0RA06212J.].
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Affiliation(s)
- Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam,Institute of Natural Products Chemistry, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Khanh B. Vu
- School of Biotechnology, International UniversityHo Chi Minh CityVietnam,Vietnam National UniversityHo Chi Minh CityVietnam
| | - T. Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang UniversityHo Chi Minh CityVietnam
| | - Le Thi Thuy Huong
- Graduate University of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam,Institute of Natural Products Chemistry, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Linh Hoang Tran
- Vietnam National UniversityHo Chi Minh CityVietnam,Faculty of Civil Engineering, Ho Chi Minh University of Technology (HCMUT)Ho Chi MinhVietnam
| | - Nguyen Thanh Tung
- Graduate University of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam,Institute of Materials Science, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh UniversityHo Chi Minh CityVietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang UniversityHo Chi Minh CityVietnam,Faculty of Applied Sciences, Ton Duc Thang UniversityHo Chi Minh CityVietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang UniversityHo Chi Minh CityVietnam,Faculty of Applied Sciences, Ton Duc Thang UniversityHo Chi Minh CityVietnam
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Nguyen HP, Tran QD, Nguyen CQ, Hoa TP, Duy Binh T, Nhu Thao H, Hue BTB, Tuan NT, Le Dang Q, Quoc Chau Thanh N, Van Ky N, Pham MQ, Yang SG. Anti-multiple myeloma potential of resynthesized belinostat derivatives: an experimental study on cytotoxic activity, drug combination, and docking studies. RSC Adv 2022; 12:22108-22118. [PMID: 36043105 PMCID: PMC9364358 DOI: 10.1039/d2ra01969h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Multiple myeloma is a deadly cancer that is a complex and multifactorial disease. In the present study, 12 belinostat derivatives (four resynthesized and eight new), HDAC inhibitors, were resynthesized via either Knoevenagel condensation, or Wittig reaction, or Heck reaction. Then an evaluation of the antiproliferative activities against myeloma cells MOPC-315 was carried out. Amongst them, compound 7f was the most bioactive compound with an IC50 of 0.090 ± 0.016 μM, being 3.5-fold more potent than the reference belinostat (IC50 = 0.318 ± 0.049 μM). Furthermore, we also confirmed the inhibitory activity of 7f in a cellular model. Additionally, we found that the inhibitory activity of 7f against histone deacetylase 6 catalytic activity (HDAC6) is more potent than that of belinostat. Finally, we observed the strong synergistic interaction between the derivative 7f and the proteasome bortezomib inhibitor (CI = 0.26), while belinostat and bortezomib showed synergism with a CI value of 0.36. Taken together, the above results suggest that 7f is a promising HDAC inhibitor deserving further investigation.
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Affiliation(s)
- Hong Phuong Nguyen
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
| | - Quang De Tran
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Cuong Quoc Nguyen
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Tran Phuong Hoa
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
| | - Tran Duy Binh
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
| | - Huynh Nhu Thao
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Bui Thi Buu Hue
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Nguyen Trong Tuan
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Quang Le Dang
- Institute for Tropical Technology, Vietnam Academy of Science and Technology Hanoi 10000 Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi 100000 Vietnam
| | - Nguyen Quoc Chau Thanh
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Nguyen Van Ky
- Department of Chemistry, College of Natural Sciences, Can Tho University Can Tho 90000 Vietnam +84934527817
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi 100000 Vietnam.,Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi 100000 Vietnam
| | - Su-Geun Yang
- Department of Biomedical Science, BK21 FOUR Program in Biomedical Science and Engineering, Inha University College of Medicine Incheon 22212 South Korea +82-32-890-1199 +82-32-890-2832
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Thai QM, Pham TNH, Hiep DM, Pham MQ, Tran PT, Nguyen TH, Ngo ST. Searching for AChE inhibitors from natural compounds by using machine learning and atomistic simulations. J Mol Graph Model 2022; 115:108230. [DOI: 10.1016/j.jmgm.2022.108230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022]
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Pham TNH, Nguyen TH, Tam NM, Y Vu T, Pham NT, Huy NT, Mai BK, Tung NT, Pham MQ, V Vu V, Ngo ST. Improving ligand-ranking of AutoDock Vina by changing the empirical parameters. J Comput Chem 2021; 43:160-169. [PMID: 34716930 DOI: 10.1002/jcc.26779] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 01/09/2023]
Abstract
AutoDock Vina (Vina) achieved a very high docking-success rate, p ^ , but give a rather low correlation coefficient, R , for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina R coefficient upon its empirical parameters. R is affected more by changing the gauss2 and rotation than other terms. The docking-success rate p ^ is sensitive to the alterations of the gauss1, gauss2, repulsion, and hydrogen bond parameters. Based on our benchmarks, the parameter set1 has been suggested to be the most optimal. The testing study over 800 complexes indicated that the modified Vina provided higher correlation with experiment R set 1 = 0.556 ± 0.025 compared with R Default = 0.493 ± 0.028 obtained by the original Vina and R Vina 1.2 = 0.503 ± 0.029 by Vina version 1.2. Besides, the modified Vina can be also applied more widely, giving R ≥ 0.500 for 32/48 targets, compared with the default package, giving R ≥ 0.500 for 31/48 targets. In addition, validation calculations for 1036 complexes obtained from version 2019 of PDBbind refined structures showed that the set1 of parameters gave higher correlation coefficient ( R set 1 = 0.617 ± 0.017 ) than the default package ( R Default = 0.543 ± 0.020 ) and Vina version 1.2 ( R Vina 1.2 = 0.540 ± 0.020 ). The version of Vina with set1 of parameters can be downloaded at https://github.com/sontungngo/mvina. The outcomes would enhance the ranking of ligand-binding affinity using Autodock Vina.
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Affiliation(s)
- T Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Minh Tam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nhat Truong Pham
- Faculty of Electrical and Electronics Engineering, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Nguyen Truong Huy
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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14
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Ngo ST, Vu KB, Pham MQ, Tam NM, Tran PT. Marine derivatives prevent wMUS81 in silico studies. R Soc Open Sci 2021; 8:210974. [PMID: 34527278 PMCID: PMC8424343 DOI: 10.1098/rsos.210974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 05/15/2023]
Abstract
The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 (wMUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent wMUS81 structure via atomistic simulations. Eight compounds such as D197 (Tryptoquivaline U), D220 (Epiremisporine B), D67 (Aspergiolide A), D153 (Preussomerin G), D547 (12,13-dihydroxyfumitremorgin C), D152 (Preussomerin K), D20 (Marinopyrrole B) and D559 (Fumuquinazoline K) were indicated that they are able to prevent the conformation of wMUS81 via forming a strong binding affinity to the enzyme via perturbation approach. The electrostatic interaction is the dominant factor in the binding process of ligands to wMUS81. The residues Trp55, Arg59, Leu62, His63 and Arg69 were found to frequently form non-bonded contacts and hydrogen bonds to inhibitors. Moreover, the influence of the ligand D197, which formed the lowest binding free energy to wMUS81, on the structural change of enzyme was investigated using replica exchange molecular dynamics simulations. The obtained results indicated that D197, which forms a strong binding affinity, can modify the structure of wMUS81. Overall, the marine compounds probably inhibit wMUS81 due to forming a strong binding affinity to the enzyme as well as altering the enzymic conformation.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Khanh B. Vu
- Department of Chemical Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen Minh Tam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Phuong-Thao Tran
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, Hanoi, Vietnam
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15
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Tran QT, Pham TD, Nguyen TD, Luu VH, Nghi Do H, Duy Le X, Nguyen PH, Nguyen MC, Luu VC, Pham MQ, Huyen Vu T, Pham TN, Pham DTN. Optimization of Murrayafoline A ethanol extraction process from the roots of Glycosmis stenocarpa, and evaluation of its Tumorigenesis inhibition activity on Hep-G2 cells. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Glycosmis stenocarpa is a species of shrub found in the Northern provinces of Vietnam. Its roots contain different carbazolic derivatives, mainly Murrayafoline A (Mu-A), which exhibits valuable biological activities. In this study, we performed an extraction of Mu-A from the roots of G. stenocarpa and optimized this process using response surface methodology (RSM) according to a central composite design, with three independent parameters including extraction time (min), extraction temperature (°C), and solvent/material ratio (mL/g). Two dependent variables were the Mu-A content (mg/g raw materials) and extraction efficiency (%). The optimal conditions to extract Mu-A were found to be as follows: extraction temperature, 67°C; extraction time, 165 min; and solvent/material ratio, 5:1. Under these conditions, the Mu-A content and extraction efficiency were 38.94 ± 1.31 mg/g raw materials and 34.98 ± 1.18%, respectively. Mu-A exhibited antiproliferation and antitumor-promoting activity against the HepG-2 cell line. The present optimization work of Mu-A extraction from G. stenocarpa roots contributed to the attempt of designing a large-scale extraction process for the compound and further exploitation of its potential in vivo applications.
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Affiliation(s)
- Quoc Toan Tran
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi 10072 , Vietnam
| | - The Dan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST) , 18 Hoang Quoc Viet, Cau Giay , Hanoi , Vietnam
| | - Thanh Duong Nguyen
- Institute of Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
| | - Van Huyen Luu
- Faculty of Environment, Hanoi University of Natural Resources and Environment , No 41A Phu Dien Road, Phu Dien Precinct, North-Tu Liem District , Hanoi , Vietnam
| | - Huu Nghi Do
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
| | - Xuan Duy Le
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
| | - Phi Hung Nguyen
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
| | - Manh Cuong Nguyen
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
| | - Van Chinh Luu
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet St., Cau Giay Dist. , Hanoi 10072 , Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi 10072 , Vietnam
| | - Thi Huyen Vu
- Faculty of Environment, Vietnam National University of Agriculture , Hanoi , Vietnam
| | - Tri Nhut Pham
- Center of Excellence for Biochemistry and Natural Products, Nguyen Tat Thanh University , Ho Chi Minh City , Vietnam
- NTT Hi-Tech Institute, Nguyen Tat Thanh University , Ho Chi Minh City , Vietnam
| | - Dung Thuy Nguyen Pham
- Center of Excellence for Biochemistry and Natural Products, Nguyen Tat Thanh University , Ho Chi Minh City , Vietnam
- NTT Hi-Tech Institute, Nguyen Tat Thanh University , Ho Chi Minh City , Vietnam
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16
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Tam NM, Pham MQ, Nguyen HT, Hong ND, Hien NK, Quang DT, Thu Phung HT, Ngo ST. Potential inhibitors for SARS-CoV-2 Mpro from marine compounds. RSC Adv 2021; 11:22206-22213. [PMID: 35480831 PMCID: PMC9034196 DOI: 10.1039/d1ra03852d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/18/2021] [Indexed: 12/26/2022] Open
Abstract
Preventing the biological activity of SARS-CoV-2 main protease using natural compounds is of great interest. In this context, using a combination of AutoDock Vina and fast pulling of ligand simulations, eleven marine fungi compounds were identified that probably play as highly potent inhibitors for preventing viral replication. In particular, four compounds including M15 (3-O-(6-O-α-l-arabinopyranosyl)-β-d-glucopyranosyl-1,4-dimethoxyxanthone), M8 (wailupemycins H), M11 (cottoquinazolines B), and M9 (wailupemycins I) adopted the predicted ligand-binding free energy of −9.87, −9.82, −9.62, and −9.35 kcal mol−1, respectively, whereas the other adopted predicted ligand-binding free energies in the range from −8.54 to −8.94 kcal mol−1. The results were obtained using a combination of Vina and FPL simulations. Notably, although, AutoDock4 adopted higher accurate results in comparison with Vina, Vina is proven to be a more suitable technique for rapidly screening ligand-binding affinity with a large database of compounds since it requires much smaller computing resources. Furthermore, FPL is better than Vina to classify inhibitors upon ROC-AUC analysis. Preventing the biological activity of SARS-CoV-2 main protease using natural compounds is of great interest.![]()
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Affiliation(s)
- Nguyen Minh Tam
- Computational Chemistry Research Group, Ton Duc Thang University Ho Chi Minh City Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam.,Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Huy Truong Nguyen
- Faculty of Pharmacy, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Nam Dao Hong
- University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City Vietnam
| | - Nguyen Khoa Hien
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam.,Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology Hue City Thua Thien Hue Province Vietnam
| | - Duong Tuan Quang
- Department of Chemistry, Hue University Hue City Thua Thien Hue Province Vietnam
| | | | - Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam.,Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
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17
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Cao DT, Huong Doan TM, Pham VC, Minh Le TH, Chae JW, Yun HY, Na MK, Kim YH, Pham MQ, Nguyen VH. Molecular design of anticancer drugs from marine fungi derivatives. RSC Adv 2021; 11:20173-20179. [PMID: 35479875 PMCID: PMC9033662 DOI: 10.1039/d1ra01855h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is one of the most potential targets in cancer therapy. We have demonstrated using a combination of molecular docking and fast pulling of ligand (FPL) simulations that marine fungi derivatives can be possible inhibitors, preventing the biological activity of Hsp90. The computational approaches were validated and compared with previous experiments. Based on the benchmark of available inhibitors of Hsp90, the GOLD docking package using the ChemPLP scoring function was found to be superior over both Autodock Vina and Autodock4 in the preliminary estimation of the ligand-binding affinity and binding pose with the Pearson correlation, R = -0.62. Moreover, FPL calculations were also indicated as a suitable approach to refine docking simulations with a correlation coefficient with the experimental data of R = -0.81. Therefore, the binding affinity of marine fungi derivatives to Hsp90 was evaluated. Docking and FPL calculations suggest that five compounds including 23, 40, 46, 48, and 52 are highly potent inhibitors for Hsp90. The obtained results enhance cancer therapy research.
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Affiliation(s)
- Duc Tuan Cao
- Hai Phong University of Medicine and Pharmacy Haiphong Vietnam
| | - Thi Mai Huong Doan
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Van Cuong Pham
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Thi Hong Minh Le
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Jung-Woo Chae
- College of Pharmacy, Chungnam National University Daejeon Republic of Korea
| | - Hwi-Yeol Yun
- College of Pharmacy, Chungnam National University Daejeon Republic of Korea
| | - Min-Kyun Na
- College of Pharmacy, Chungnam National University Daejeon Republic of Korea
| | - Young-Ho Kim
- College of Pharmacy, Chungnam National University Daejeon Republic of Korea
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Van Hung Nguyen
- Hai Phong University of Medicine and Pharmacy Haiphong Vietnam
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18
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Abstract
The COVID-19 pandemic has killed millions of people worldwide since its outbreak in December 2019. The pandemic is caused by the SARS-CoV-2 virus whose main protease (Mpro) is a promising drug target since it plays a key role in viral proliferation and replication. Currently, developing an effective therapy is an urgent task, which requires accurately estimating the ligand-binding free energy to SARS-CoV-2 Mpro. However, it should be noted that the accuracy of a free energy method probably depends on the protein target. A highly accurate approach for some targets may fail to produce a reasonable correlation with the experiment when a novel enzyme is considered as a drug target. Therefore, in this context, the ligand-binding affinity to SARS-CoV-2 Mpro was calculated via various approaches. The molecular docking approach was manipulated using Autodock Vina (Vina) and Autodock4 (AD4) protocols to preliminarily investigate the ligand-binding affinity and pose to SARS-CoV-2 Mpro. The binding free energy was then refined using the fast pulling of ligand (FPL), linear interaction energy (LIE), molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA), and free energy perturbation (FEP) methods. The benchmark results indicated that for docking calculations, Vina is more accurate than AD4, and for free energy methods, FEP is the most accurate method, followed by LIE, FPL, and MM-PBSA (FEP > LIE ≈ FPL > MM-PBSA). Moreover, atomistic simulations revealed that the van der Waals interaction is the dominant factor. The residues Thr26, His41, Ser46, Asn142, Gly143, Cys145, His164, Glu166, and Gln189 are essential elements affecting the binding process. Our benchmark provides guidelines for further investigations using computational approaches.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational
Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000,
Vietnam
- Faculty of Applied Sciences, Ton Duc
Thang University, Ho Chi Minh City 700000,
Vietnam
| | - Nguyen Minh Tam
- Faculty of Applied Sciences, Ton Duc
Thang University, Ho Chi Minh City 700000,
Vietnam
- Computional Chemistry Research Group, Ton
Duc Thang University, Ho Chi Minh City 700000,
Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology,
Vietnam Academy of Science and Technology, Hanoi 100000,
Vietnam
- Institute of Natural Products Chemistry,
Vietnam Academy of Science and Technology, Hanoi 100000,
Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational
Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000,
Vietnam
- Faculty of Applied Sciences, Ton Duc
Thang University, Ho Chi Minh City 700000,
Vietnam
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19
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Tran LT, Le TM, Nguyen TM, Tran QT, Le XD, Pham MQ, Lam VT, Van Do M. Simultaneous removal efficiency of H2S and CO2 by high-gravity rotating packed bed: Experiments and simulation. OPEN CHEM 2021. [DOI: 10.1515/chem-2020-0187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
This study explores the possibility of applying high-gravity rotating packed bed (HGRPB) in removing H2S and CO2 from biogas. Ca(OH)2 aqueous solution was used as the absorbent in this study. Different experimental conditions including solution pH, rotating speed (R
S) of HGRPB, gas flow rate (Q
G), and liquid flow rate (Q
L) were investigated with respect to the removal efficiency (E) of H2S and CO2. The experimental and simulated results show that the optimal removal efficiency of H2S and CO2 using HGRPB achieved nearly the same as 99.38 and 99.56% for removal efficiency of H2S and 77.28 and 77.86% for removal efficiency of CO2, respectively. Such efficiencies corresponded with the following optimal conditions: a solution pH of 12.26, HGRPB reactor with the rotating speed of 1,200 rpm, the gas flow rate of 2.46 (L/min), and the liquid flow rate of 0.134 (L/min).
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Affiliation(s)
- Lien Thi Tran
- Institute of Environmental Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
| | - Tuan Minh Le
- Institute of Environmental Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
| | - Tuan Minh Nguyen
- Institute of Environmental Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
| | - Quoc Toan Tran
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
| | - Xuan Duy Le
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
| | - Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
| | - Van Tan Lam
- NTT Hi-Tech Institute, Nguyen Tat Thanh University , Ho Chi Minh City , 755414 , Vietnam
- Center of Excellence for Green Energy and Environmental Nanomaterials, Nguyen Tat Thanh University , Ho Chi Minh City , Vietnam
| | - Manh Van Do
- Institute of Environmental Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cau Giay , Hanoi , 100000 , Vietnam
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20
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Leng J, Xu H, Schaenzer M, Quan Pham M, Bourgeois G, Shanian A, Pasini D. Generalized tessellations of superellipitcal voids in low porosity architected materials for stress mitigation. Proc Math Phys Eng Sci 2021. [DOI: 10.1098/rspa.2020.0864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Stress concentration is a crucial source of mechanical failure in structural elements, especially those embedding voids. This paper examines periodic porous materials with porosity lower than 5%. We investigate their stress distribution under planar multiaxial loading, and presents a family of geometrically optimized void shapes for stress mitigation. We adopt a generalized description for both void geometry and planar tessellation patterns that can handle single and multiple voids of arbitrary void shape at a generic angle. The role of void shape evolution from diamond to rectellipse on the stress-distribution is captured at the edge of voids in a representative volume element (RVE) made of non-equal length periodic vectors. Theoretical derivations, numerical simulations along with experimental validation of the strain field in thermoplastic polymer samples fabricated by laser cutting unveil the role of geometric parameters, e.g. superellipse order, aspect ratio and rotation angle, that minimize stress peak and ameliorate stress distribution around voids. This work extends and complements classical theory by providing fundamental insights into the role that tessellation, void shape and inclination play in the stress distribution of low-porosity architected materials, thus introducing essential guidelines of broad application for stress-minimization and failure mitigation in diverse sectors.
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Affiliation(s)
- Jiazhen Leng
- Department of Mechanical Engineering, McGill University, 817 Sherbrooke Street West, Montreal QC H3A 0C3, Canada
| | - Hang Xu
- Department of Mechanical Engineering, McGill University, 817 Sherbrooke Street West, Montreal QC H3A 0C3, Canada
| | - Megan Schaenzer
- Siemens Power and Gas, 9545 Côte-de-Liesse, Dorval, QC H9P 1A5, Canada
| | - Minh Quan Pham
- Siemens Power and Gas, 9545 Côte-de-Liesse, Dorval, QC H9P 1A5, Canada
| | | | - Ali Shanian
- Siemens Power and Gas, 9545 Côte-de-Liesse, Dorval, QC H9P 1A5, Canada
| | - Damiano Pasini
- Department of Mechanical Engineering, McGill University, 817 Sherbrooke Street West, Montreal QC H3A 0C3, Canada
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21
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Tam NM, Pham MQ, Ha NX, Nam PC, Phung HTT. Computational estimation of potential inhibitors from known drugs against the main protease of SARS-CoV-2. RSC Adv 2021; 11:17478-17486. [PMID: 35479689 PMCID: PMC9032918 DOI: 10.1039/d1ra02529e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022] Open
Abstract
The coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide recently, leading to global social and economic disruption. Although the emergently approved vaccine programs against SARS-CoV-2 have been rolled out globally, the number of COVID-19 daily cases and deaths has remained significantly high. Here, we attempt to computationally screen for possible medications for COVID-19 via rapidly estimating the highly potential inhibitors from an FDA-approved drug database against the main protease (Mpro) of SARS-CoV-2. The approach combined molecular docking and fast pulling of ligand (FPL) simulations that were demonstrated to be accurate and suitable for quick prediction of SARS-CoV-2 Mpro inhibitors. The results suggested that twenty-seven compounds were capable of strongly associating with SARS-CoV-2 Mpro. Among them, the seven top leads are daclatasvir, teniposide, etoposide, levoleucovorin, naldemedine, cabozantinib, and irinotecan. The potential application of these drugs in COVID-19 therapy has thus been discussed. Approved drugs predicted to interact with critical residues in the substrate-binding site of SARS-CoV-2 Mpro can be promising inhibitors.![]()
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Affiliation(s)
- Nguyen Minh Tam
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Minh Quan Pham
- Institute of Natural Products Chemistry
- Vietnam Academy of Science and Technology
- Hanoi
- Vietnam
- Graduate University of Science and Technology
| | - Nguyen Xuan Ha
- Faculty of Chemistry and Environment
- Thuyloi University
- Ministry of Agriculture and Rural Development
- Hanoi
- Vietnam
| | - Pham Cam Nam
- Department of Chemical Engineering
- The University of Da Nang
- University of Science and Technology
- Da Nang City
- Vietnam
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22
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Tabrizi L, Nguyen TLA, Tran HDT, Pham MQ, Dao DQ. Antioxidant and Anticancer Properties of Functionalized Ferrocene with Hydroxycinnamate Derivatives-An Integrated Experimental and Theoretical Study. J Chem Inf Model 2020; 60:6185-6203. [PMID: 33233887 DOI: 10.1021/acs.jcim.0c00730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two ferrocenyl derivatives, Fc-CA and Fc-FA, were synthesized by a condensation reaction between the amino ferrocene and hydroxycinnamic acids, that is, caffeic acid (CA) and ferulic acid (FA). The structures and purity of all compounds were characterized by 1H- and 13C NMR spectroscopies, Mass spectrometry (MS), and elemental analysis. The antioxidant properties of Fc-CA and Fc-FA and of its ligand were studied for free radical scavenging activity toward DPPH•, superoxide anion (O2•-), NO•, and ABTS•+ by UV-vis and electron spin resonance spectroscopies. The cytotoxicity of Fc-CA and Fc-FA against MCF-7 and MDA-MB-231 breast cancer cells and MRC-5 human lung fibroblasts cell was higher than that of cisplatin. The geometry and electronic structures of all compounds were then simulated using density functional theory at M05-2X/6-311+G(d,p) level of theory. Thermodynamics of the free radical quenching reactions by common mechanisms reveal the higher antioxidant properties of the Fc-CA and Fc-FA in comparison to their ligands. An in-depth study of the free radical scavenging activity against HOO• and HO• radicals was performed for two of the most favorable and competitive mechanisms, the hydrogen transfer (either hydrogen atom transfer or proton-coupled electron transfer mechanisms) and the radical adduct formation. The in silico studies indicated that ferrocenyl derivatives exhibited prominent binding affinity to protein models in comparison to CA and FA. Their dock scores were notable at ligand binding sites of ERα, Erβ, and JAK2 proteins. Dock pose analysis also shed light into the possible mechanism of action for the studied compounds.
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Affiliation(s)
- Leila Tabrizi
- School of Chemistry, National University of Ireland, Galway, University Road, Galway H91 TK33, Ireland
| | - Thi Le Anh Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam.,Faculty of Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | | | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
| | - Duy Quang Dao
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
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23
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Pham MQ, Le TTH, Do TL, Pham THM, Pham QL, Nguyen PH, To DC. Identification of Cytotoxic Constituents from the Whole Plant of Isodon ternifolius. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20953243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A new oxygenated spiroketone, isodonspiroketone (1), and 4 known ones (2-5) were isolated from the whole plant of Isodon ternifolius (D.Don) Kudô. The structure of isodonspiroketone (1) was determined by nuclear magnetic resonance, mass spectroscopy, and circular dichroism spectral data. Compound 3 has not been previously isolated from I. ternifolius. Their cytotoxic activities were evaluated against A549, HepG2, and MDA-MB-231 cancer cell lines in vitro. New compound (isodonspiroketone, 1) showed moderate cytotoxic activities against A549, HepG2, and MDA-MB-231 cancer cell lines with half-maximal inhibitory concentration values of 23.84 ± 2.73, 27.77 ± 3.01, and 17.26 ± 1.61 μM, respectively; meanwhile, the others were inactive.
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Affiliation(s)
- Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology, VAST, Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi-Thuy-Huong Le
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology, VAST, Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Tien-Lam Do
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology, VAST, Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi-Hong-Minh Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology, VAST, Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Quoc-Long Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Phi-Hung Nguyen
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology, VAST, Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Dao-Cuong To
- Faculty of Pharmacy, Phenikaa University, Yen Nghia, Ha Dong district, Hanoi, Vietnam
- Phenikaa Research and Technology Institute (PRATI), A&A Green Phoenix Group JSC, Hoang Ngan, Cau Giay district, Hanoi, Vietnam
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Pham MQ, Vu KB, Han Pham TN, Thuy Huong LT, Tran LH, Tung NT, Vu VV, Nguyen TH, Ngo ST. Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations. RSC Adv 2020; 10:31991-31996. [PMID: 35518150 PMCID: PMC9056572 DOI: 10.1039/d0ra06212j] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/10/2020] [Indexed: 01/30/2023] Open
Abstract
Originating for the first time in Wuhan, China, the outbreak of SARS-CoV-2 has caused a serious global health issue. An effective treatment for SARS-CoV-2 is still unavailable. Therefore, in this study, we have tried to predict a list of potential inhibitors for SARS-CoV-2 main protease (Mpro) using a combination of molecular docking and fast pulling of ligand (FPL) simulations. The approaches were initially validated over a set of eleven available inhibitors. Both Autodock Vina and FPL calculations produced consistent results with the experiments with correlation coefficients of R Dock = 0.72 ± 0.14 and R W = -0.76 ± 0.10, respectively. The combined approaches were then utilized to predict possible inhibitors that were selected from a ZINC15 sub-database for SARS-CoV-2 Mpro. Twenty compounds were suggested to be able to bind well to SARS-CoV-2 Mpro. Among them, five top-leads are periandrin V, penimocycline, cis-p-Coumaroylcorosolic acid, glycyrrhizin, and uralsaponin B. The obtained results could probably lead to enhance the COVID-19 therapy.
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Affiliation(s)
- Minh Quan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Khanh B Vu
- School of Biotechnology, International University Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City Vietnam
| | - T Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Le Thi Thuy Huong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Linh Hoang Tran
- Vietnam National University Ho Chi Minh City Vietnam
- Faculty of Civil Energeering, Ho Chi Minh University of Technology (HCMUT) Ho Chi Minh Vietnam
| | - Nguyen Thanh Tung
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
- Institute of Materials Science, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University Ho Chi Minh City Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
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25
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Nguyen NT, Nguyen TH, Pham TNH, Huy NT, Bay MV, Pham MQ, Nam PC, Vu VV, Ngo ST. Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity. J Chem Inf Model 2019; 60:204-211. [DOI: 10.1021/acs.jcim.9b00778] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nguyen Thanh Nguyen
- Department of Theoretical Physics, Ho Chi Minh City University of Science, Ho Chi Minh City 700000, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - T. Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Truong Huy
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Mai Van Bay
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City 550000, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
| | - Pham Cam Nam
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City 550000, Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
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26
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Nguyen PH, Tuan HN, Hoang DT, Vu QT, Pham MQ, Tran MH, To DC. Glucose Uptake Stimulatory and PTP1B Inhibitory Activities of Pimarane Diterpenes from Orthosiphon stamineus Benth. Biomolecules 2019; 9:biom9120859. [PMID: 31835878 PMCID: PMC7017366 DOI: 10.3390/biom9120859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 11/16/2022] Open
Abstract
Seven pimarane diterpenes (1–7) were isolated from Orthosiphon stamineus Benth. by assay-guided isolation. All of the isolates possessed a 2-deoxy-2-((7-nitro-2,1,3-benzoxadiazol-4-yl)amino)-d-glucose uptake effect in 3T3-L1 adipocytes at concentrations of 5 and 10 μM. Most of them showed potent inhibition against protein tyrosine phosphatase 1B with IC50 values ranging from 0.33 to 9.84 μM. In the kinetic study, all inhibition types were exposed for the examined potencies, including mixed-competitive (1), non-competitives (3 and 5), competitive (6), and uncompetitive (7). The results suggested that O. stamineus and its pimarane diterpenes might exert the hypoglycemic effect via the insulin signaling pathway targeting inhibition of protein tyrosine phosphatase 1B (PTP1B) activity.
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Affiliation(s)
- Phi Hung Nguyen
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 122100, Vietnam;
- Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet, Cau Giay, Hanoi 122100, Vietnam
- Correspondence: (P.H.N.); (D.C.T.)
| | - Huynh Nhu Tuan
- Faculty of Pharmacy, Dong A University, 33 Xo Viet Nghe Tinh, Hai Chau District, Da Nang 550000, Vietnam;
| | - Duc Thuan Hoang
- Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi 123106, Vietnam; (D.T.H.); (Q.T.V.)
| | - Quoc Trung Vu
- Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi 123106, Vietnam; (D.T.H.); (Q.T.V.)
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi 122100, Vietnam;
- Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet, Cau Giay, Hanoi 122100, Vietnam
| | - Manh Hung Tran
- Biomedical Sciences Department, Institute for Research & Executive Education (VNUK), The University of Danang, 158A Le Loi, Hai Chau, Danang 551000, Vietnam;
| | - Dao Cuong To
- Faculty of Pharmacy, Phenikaa University, Yen Nghia, Ha Dong, Hanoi 12116, Vietnam
- Phenikaa Research and Technology Institute (PRATI), A&A Green Phoenix Group JSC, No.167 Hoang Ngan, Trung Hoa, Cau Giay, Hanoi 11313, Vietnam
- Correspondence: (P.H.N.); (D.C.T.)
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Doan DT, Luu DP, Nguyen TD, Hoang Thi B, Pham Thi HM, Do HN, Luu VH, Pham TD, Than VT, Pham Thi HH, Pham MQ, Tran QT. Isolation of Penicillium citrinum from Roots of Clerodendron cyrtophyllum and Application in Biosynthesis of Aglycone Isoflavones from Soybean Waste Fermentation. Foods 2019; 8:foods8110554. [PMID: 31698736 PMCID: PMC6915340 DOI: 10.3390/foods8110554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/24/2019] [Accepted: 10/28/2019] [Indexed: 11/16/2022] Open
Abstract
Soybeans offer an abundant source of isoflavones, which confer useful bioactivities when existing in aglycone forms. The conversion of isoflavones into aglycones via fermentation of soybean products is often realized by β-glucosidase, an enzyme produced by fungi. In this study, a filamentous fungus, Clerodendron cyrtophyllum, was isolated from root of Clerodendron cyrtophyllum Turcz, which was able to produce the highest activity of β-glucosidase up to 33.72 U/mL at 144 h during fermentation on Potato Dextrose Broth (PDB). The obtained fungus was grown on isoflavones-rich soybean extract to produce genistein and daidzein, achieving the conversion rate of 98.7%. Genistein and daidzein were isolated and purified by column chromatography using hexane/acetone (29:1/1:1), reaching purities of over 90% of total isoflavones, as identified and determined by TLC, LC-MS/MS, and 1H and 13C NMR spectroscopy. These results imply that the isolated P. citrinum is a potential fungal strain for industrial-scale production of genistein and daidzein from isoflavones-containing soybean extracts. These products may serve as potential raw materials for manufacture of functional foods that are based on aglycones.
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Affiliation(s)
- Duy Tien Doan
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (D.T.D.); (D.P.L.); (T.D.N.)
| | - Duc Phuong Luu
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (D.T.D.); (D.P.L.); (T.D.N.)
| | - Thanh Duong Nguyen
- Institute of Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (D.T.D.); (D.P.L.); (T.D.N.)
| | - Bich Hoang Thi
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology,18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (B.H.T.); (H.M.P.T.); (H.N.D.); (T.D.P.); (M.Q.P.)
| | - Hong Minh Pham Thi
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology,18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (B.H.T.); (H.M.P.T.); (H.N.D.); (T.D.P.); (M.Q.P.)
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam
| | - Huu Nghi Do
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology,18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (B.H.T.); (H.M.P.T.); (H.N.D.); (T.D.P.); (M.Q.P.)
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam
| | - Van Huyen Luu
- Hanoi University of Natural Resources and Environment, Hanoi 10072, Vietnam;
| | - The Dan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology,18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (B.H.T.); (H.M.P.T.); (H.N.D.); (T.D.P.); (M.Q.P.)
- Vietnam Academy of Science and Technology, University of Science and Technology of Hanoi, Hanoi 10072, Vietnam
| | - Van Thai Than
- NTT Institute of High Technology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam;
| | - Hai Ha Pham Thi
- Faculty of Biotechnology, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
- Correspondence: (H.H.P.T.); (Q.T.T.)
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology,18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (B.H.T.); (H.M.P.T.); (H.N.D.); (T.D.P.); (M.Q.P.)
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam
| | - Quoc Toan Tran
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology,18 Hoang Quoc Viet St., Cau Giay Dist., Hanoi 10072, Vietnam; (B.H.T.); (H.M.P.T.); (H.N.D.); (T.D.P.); (M.Q.P.)
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam
- Correspondence: (H.H.P.T.); (Q.T.T.)
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Nguyen THV, Tran TT, Cam TI, Pham MQ, Pham QL, Vu DH, Nguyen XN, Chau VM, Van KP. Alkaloids From Zanthoxylum nitidum and Their Cytotoxic Activity. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19844133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Zanthoxylum nitidum (Roxb.) DC (Rutaceae) is a traditional medicine used for the treatment of various diseases like toothache, gingivitis, fever, colic vomiting, diarrhea, and cholera. Three new alkaloids, zanthocadinanine C (1), 7-methoxy-8-demethoxynitidine (2), and zanthonitiside I (3) were isolated from the stems and twigs of Z. nitidum. Their structures were determined on the basis of extensive spectroscopic, including 1-dimensional and 2-dimensional nuclear magnetic resonance and mass spectroscopy data. Compounds 1–3 were evaluated for cytotoxic activity against 5 human cancer cell lines, KB, MCF-7, LNCaP, HepG-2, and LU-1. Compound 2 showed significant cytotoxic activity against all tested human cancer cell lines with IC50 values ranging from 10.3 to 12.6 µM.
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Affiliation(s)
- Thi Hong Van Nguyen
- Institute of Natural Product Chemistry, Vietnam Academy of Science and Technology (VAST), Cau Giay, Hanoi, Vietnam
| | - Thi Tuyen Tran
- Institute of Natural Product Chemistry, Vietnam Academy of Science and Technology (VAST), Cau Giay, Hanoi, Vietnam
| | - Thi Inh Cam
- Institute of Natural Product Chemistry, Vietnam Academy of Science and Technology (VAST), Cau Giay, Hanoi, Vietnam
| | - Minh Quan Pham
- Institute of Natural Product Chemistry, Vietnam Academy of Science and Technology (VAST), Cau Giay, Hanoi, Vietnam
| | - Quoc Long Pham
- Institute of Natural Product Chemistry, Vietnam Academy of Science and Technology (VAST), Cau Giay, Hanoi, Vietnam
| | - Dinh Hoang Vu
- Hanoi University of Science and Technology, Hai Ba Trung, Hanoi, Vietnam
| | | | - Van Minh Chau
- Institute of Marine Biochemistry, VAST, Cau Giay, Hanoi, Vietnam
| | - Kiem Phan Van
- Institute of Marine Biochemistry, VAST, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
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29
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Tran QT, Le TTT, Pham MQ, Do TL, Vu MH, Nguyen DC, Bach LG, Bui LM, Pham QL. Fatty Acid, Lipid Classes and Phospholipid Molecular Species Composition of the Marine Clam Meretrix lyrata (Sowerby 1851) from Cua Lo Beach, Nghe An Province, Vietnam. Molecules 2019; 24:molecules24050895. [PMID: 30836630 PMCID: PMC6429517 DOI: 10.3390/molecules24050895] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 02/07/2023] Open
Abstract
This study aims to analyze compositions of fatty acids and phospholipid molecular species in the hard clams Meretrix lyrata (Sowerby, 1851) harvested from Cua Lo beach, Nghe An province, Viet Nam. Total lipid of hard clams Meretrix lyrata occupied 1.7 ± 0.2% of wet weight and contained six classes: hydrocarbon and wax (HW), triacylglycerol (TAG), free fatty acids (FFA), sterol (ST), polar lipid (PoL), and monoalkyl diacylglycerol (MADAG). Among the constituents, the proportion of PoL accounted was highest, at 45.7%. In contrast, the figures for MADAG were lowest, at 1.3%. Twenty-six fatty acids were identified with the ratios of USAFA/SAFA was 2. The percentage of n-3 PUFA (ω-3) and n-6 PUFA (ω-6) was high, occupying 38.4% of total FA. Among PUFAs, arachidonic acid (AA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3), docosapentaenoic acid (DPA, 22:5n-3), and docosahexaenoic acid (DHA, 22:6n-3) accounted for 3.8%, 7.8%, 2.2% and 12.0% of total lipid of the clam respectively. Phospholipid molecular species were identified in polar lipids of the clams consisting six types: phosphatidylethalnolamine (PE, with 28 molecular species), phosphatidylcholine (PC, with 26 molecular species), phosphatidylserine (PS, with 18 molecular species), phosphatidylinositol (PI, with 10 molecular species), phosphatidylglycerol (PG, with only one molecular species), and ceramide aminoethylphosphonate (CAEP, with 15 molecular species). This is the first time that the molecular species of sphingophospholipid were determined, in Meretrix lyrata in particular, and for clams in general. Phospholipid formula species of PE and PS were revealed to comprise two kinds: Alkenyl acyl glycerophosphoethanolamine and Alkenyl acyl glycerophosphoserine occupy 80.3% and 81.0% of total PE and PS species, respectively. In contrast, the percentage of diacyl glycero phosphatidylcholine was twice as high as that of PakCho in total PC, at 69.3, in comparison with 30.7%. In addition, phospholipid formula species of PI and PG comprised only diacyl glycoro phospholipids. PE 36:1 (p18:0/18:1), PC 38:6 (16:0/22:6), PS 38:1 (p18:0/20:1), PI 40:5 (20:1/20:4), PG 32:0 (16:0/16:0) and CAEP 34:2 (16:2/d18:0) were the major molecular species.
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Affiliation(s)
- Quoc Toan Tran
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
| | - Thi Thanh Tra Le
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
- Department of Chemical Engineering, Faculty of Environment, Thuy loi University, Hanoi 122100, Vietnam.
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
| | - Tien Lam Do
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
| | - Manh Hung Vu
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
| | - Duy Chinh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam.
| | - Long Giang Bach
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam.
- Center of Excellence for Biochemistry and Natural Products, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam.
| | - Le Minh Bui
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam.
| | - Quoc Long Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 122100, Vietnam.
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30
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Pham MQ, Tran THV, Pham QL, Gairin JE. In silico analysis of the binding properties of solasonine to mortalin and p53, and in vitro pharmacological studies of its apoptotic and cytotoxic effects on human HepG2 and Hep3b hepatocellular carcinoma cells. Fundam Clin Pharmacol 2019; 33:385-396. [DOI: 10.1111/fcp.12447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 01/07/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Minh Quan Pham
- UPS UMR 152 Pharma‐DEV Université Toulouse 3 Faculté des Sciences Pharmaceutiques Université de Toulouse 35 Chemin des Maraîchers F‐31062 Toulouse France
- Institute of Natural Products Chemistry Vietnam Academy of Science and Technology Building 1H, 18 Hoang Quoc Viet Hanoi Vietnam
| | - Thi Hoai Van Tran
- Institute of Natural Products Chemistry Vietnam Academy of Science and Technology Building 1H, 18 Hoang Quoc Viet Hanoi Vietnam
- Vietnam Academy of Science and Technology Graduate University of Science and Technology 18 Hoang Quoc Viet Hanoi Vietnam
- Vietnam University of Traditional Medicine Ministry of Health 2 Tran Phu Hanoi Vietnam
| | - Quoc Long Pham
- Institute of Natural Products Chemistry Vietnam Academy of Science and Technology Building 1H, 18 Hoang Quoc Viet Hanoi Vietnam
| | - Jean Edouard Gairin
- UPS UMR 152 Pharma‐DEV Université Toulouse 3 Faculté des Sciences Pharmaceutiques Université de Toulouse 35 Chemin des Maraîchers F‐31062 Toulouse France
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31
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Thida M, Kim DW, Tran TTT, Pham MQ, Lee H, Kim I, Lee JW. Gambogic acid induces apoptotic cell death in T98G glioma cells. Bioorg Med Chem Lett 2016; 26:1097-1101. [DOI: 10.1016/j.bmcl.2015.11.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/10/2015] [Accepted: 11/14/2015] [Indexed: 10/22/2022]
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32
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Pham MQ, Iscache AL, Pham QL, Gairin JE. Cytotoxic, apoptotic, and sensitization properties ofent-kaurane-type diterpenoids fromCroton tonkinensisGagnep on human liver cancer HepG2 and Hep3b cell lines. Fundam Clin Pharmacol 2016; 30:137-46. [DOI: 10.1111/fcp.12176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/16/2015] [Accepted: 12/23/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Minh Quan Pham
- Faculté des Sciences Pharmaceutiques; UPS; UMR 152 Pharma-DEV; Université de Toulouse; Université Toulouse 3 35 Chemin des Maraîchers Toulouse Cedex 9 F-31062 France
- Institute of Natural Products Chemistry; Vietnam Academy of Science and Technology; Building 1H 18 Hoang Quoc Viet Hanoi Vietnam
| | - Anne Laure Iscache
- Plateau technique de cytométrie et tri cellulaire; UMR INSERM 1043-CNRS 5282- Université Toulouse 3; CHU Purpan BP3028 31024 Toulouse Cedex 3 France
| | - Quoc Long Pham
- Institute of Natural Products Chemistry; Vietnam Academy of Science and Technology; Building 1H 18 Hoang Quoc Viet Hanoi Vietnam
| | - Jean Edouard Gairin
- Faculté des Sciences Pharmaceutiques; UPS; UMR 152 Pharma-DEV; Université de Toulouse; Université Toulouse 3 35 Chemin des Maraîchers Toulouse Cedex 9 F-31062 France
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33
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Bourne AR, Mohan G, Stone MF, Pham MQ, Schultz CR, Meyerhoff JL, Lumley LA. Olfactory cues increase avoidance behavior and induce Fos expression in the amygdala, hippocampus and prefrontal cortex of socially defeated mice. Behav Brain Res 2013; 256:188-96. [PMID: 23968590 DOI: 10.1016/j.bbr.2013.08.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/10/2013] [Accepted: 08/13/2013] [Indexed: 11/29/2022]
Abstract
Genes and proteins of the Fos family are used as markers of neuronal activity and can be modulated by stress. This study investigated whether social defeat (SD) or exposure to an olfactory cue associated with the SD experience activated Fos and FosB/DeltaFosB (ΔFosB) expression in brain regions implicated in the development of post-traumatic stress disorder. Mice exposed to acute SD showed more Fos positive cells in the basolateral amygdala (BLA), CA1 of the hippocampus and the medial prefrontal cortex (mPFC) 1h after SD, and had greater expression of the more persistent FosB/ΔFosB protein in the BLA 24 h after SD compared to controls. Mice exposed to an olfactory cue 24 h or 7 days after SD had higher levels of Fos expression in all three regions 1h after exposure to the cue, and displayed increased avoidance behavior compared to controls. While the avoidance response dissipated with time (less at 7 day vs 24 h after social defeat), Fos expression in the mPFC and CA1 in response to an olfactory cue was greater at 7 days relative to 24 h after social defeat. The results suggest additional processing of the cue-stress association and may provide further support for a role of the mPFC in fear inhibition. These findings may have implications for brain regions and circuitry involved in the avoidance of cues associated with a stressful event that may lead to context-dependent adaptive or maladaptive behavior.
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Affiliation(s)
- A R Bourne
- US Army Medical Research Institute of Chemical Defense, Aberdeen Proving Ground, MD 21010-5400, USA
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34
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Abstract
Many eukaryotic proteins have been successfully expressed in insect cells infected with a recombinant baculovirus derived from the Autographa californica nuclear polyhedrosis virus (AcNPV). There are, however, disadvantages with this cell-based system when carried out in suspension cultures at high bioreactor volume (e.g., limited oxygen transfer, susceptibility to contamination, high cost). These problems can be avoided by using whole larvae as the "reactors." There are, however, other problems encountered with larvae, one being their inaccessibility for product sampling. To combat this problem, we have investigated the expression of green fluorescent protein (GFP) as a reporter molecule in Trichoplusia ni insect larvae. A high production level of GFPuv (1.58 mg per larva, 26% of total protein) was obtained, enabling the rapid and non-invasive monitoring of GFP. Bright green light was emitted directly from the large opaque carcasses ( approximately 30mm) after illumination with UV light. Based on the green light intensity and a correlation between intensity and GFP mass, we determined the optimal harvest time (c.a. approximately 3 days post-infection). In parallel experiments, we expressed human interleukin-2 (IL-2) from another recombinant baculovirus with an almost identical expression profile. Since both GFP and IL-2 were rapidly degraded by protease activity during the fourth day post-infection (another disadvantage with larvae), we found an accurate determination of harvest time was critical. Correspondingly, our results demonstrated that GFP was an effective on-line marker for expression of heterologous protein in insect larvae.
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Affiliation(s)
- H J Cha
- Center for Agricultural Biotechnology, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
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Cha HJ, Dalal NG, Pham MQ, Kramer SF, Vakharia VN, Bentley WE. Monitoring foreign protein expression under baculovirus p10 and polh promoters in insect larvae. Biotechniques 2002; 32:986, 988, 990 passim. [PMID: 12019794 DOI: 10.2144/02325bm02] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- H J Cha
- University of Maryland, College Park 20742, USA
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Abstract
The insect larvae/baculovirus protein production process was dramatically simplified by expressing fusion proteins containing green fluorescent protein (GFP) and the product-of-interest. In this case, human interleukin-2 (hIL-2) and chloramphenicol acetyl-transferase (CAT) were model products. Specifically, our fusion construct was comprised of a histidine affinity ligand for simplified purification using immobilized metal affinity chromatography (IMAC), the UV-optimized GFP (GFPuv) as a marker, an enterokinase cleavage site for recovery of the product from the fusion, and the product, hIL-2 or CAT. Both the approximately 52 kDa GFPuv/hIL-2 and approximately 63 kDa GFPuv/CAT fusions were expressed in Trichoplusia ni larvae at 9.0 microg-hIL-2 and 24.1 microg-CAT per larva, respectively. The GFP enabled clear identification of the infection process, harvest time, and more importantly, the quantity of product protein. Because the GFP served as a marker, this technique obviates the need for in-process Western analyses (during expression, separation, and purification stages). As a purification marker, GFP facilitated rapid identification of product-containing elution fractions (Cha et al., 1999b), as well as product-containing waste fractions (e.g., cell pellet). Also, because the fluorescence intensity was linear with hIL-2 and CAT, we were able to select the highest-producing larvae. That is, three fold more product was found in the brightest larva compared to the average. Finally, because the GFP is attached to the product protein and the producing larvae can be selected, the infection and production processes can be made semi-continuous or continuous, replacing the current batch process. These advantages should help to enable commercialization of larvae as expression hosts.
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Affiliation(s)
- H J Cha
- Center for Agricultural Biotechnology, University of Maryland Biotechnology Institute, USA
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Cha HJ, Dalal NG, Pham MQ, Bentley WE. Purification of human interleukin-2 fusion protein produced in insect larvae is facilitated by fusion with green fluorescent protein and metal affinity ligand. Biotechnol Prog 1999; 15:283-6. [PMID: 10194406 DOI: 10.1021/bp990022t] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fusion protein of green fluorescent protein (GFP) and human interleukin-2 (hIL-2) was produced in insect Trichoplusia ni larvae infected with recombinant baculovirus derived from the Autographa californica nuclear polyhedrosis virus (AcNPV). This fusion protein was composed of a metal ion binding site (His)6 for rapid one-step purification using immobilized metal affinity chromatography (IMAC), UV-optimized GFP (GFPuv), enterokinase cleavage site for recovering hIL-2 from purified fusion protein, and hIL-2 protein. The additional histidine residues on fusion protein enabled the efficient purification of fusion protein based on immobilized metal affinity chromatography. In addition to advantages of GFP as a fusion marker, GFP was able to be used as a selectable purification marker; we easily determined the correct purified fusion protein sample fraction by simply detecting GFP fluorescence.
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Affiliation(s)
- H J Cha
- Department of Chemical Engineering, University of Maryland, and Center for Agricultural Biotechnology, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
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38
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Abstract
Many eukaryotic proteins have been successfully expressed in insect cells infected with a baculovirus in which the foreign gene has been placed under the control of a viral promoter. This system can be costly at large scale due to the quality of virus stock, problems of oxygen transfer, and severity of large-scale contamination. To circumvent this problem, we have investigated the expression of a foreign protein, human interleukin-2 (IL-2), in insect larvae, Trichoplusia ni, infected with the baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV). The IL-2 gene was placed under control of the p10 promoter so that the polyhedra remained intact for efficient primary infection. From our results, it was clear that early infection limited larval growth and late infection delayed product production until near pupation, hence infection timing was important. Also, the harvest time was crucial for obtaining high yield, because IL-2 production had a sharp optimal peak with a time of occurrence dependent on both temperature and the initial amount of infection virus. Specifically, we found that, by raising the infection temperature to 30 degrees C, we more than doubled the protein productivity. Furthermore, a significant concern of the larvae/baculovirus expression system has been the large amount of protease produced by the larvae, which adversely affects the protein yield. Therefore, we screened several protease inhibitors and characterized the larval protease specificity and timing to attenuate their impact. This report elucidates and delineates the factors that most directly impact protein yield in the larvae expression system, using IL-2 as a model.
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Affiliation(s)
- M Q Pham
- Center for Agricultural Biotechnology, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
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Lee T, Pham MQ, Weigand WA, Harvey SP, Bentley WE. Bioreactor strategies for the treatment of growth-inhibitory waste: an analysis of thiodiglycol degradation, the main hydrolysis product of sulfur mustard. Biotechnol Prog 1996; 12:533-9. [PMID: 8987480 DOI: 10.1021/bp9600290] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The microbial degradation of thiodiglycol, the primary hydrolysis product of sulfur mustard, by a pure culture of Alcaligenes xylosoxydans ssp. xylosoxydans (SH91) was accomplished in laboratory scale stirred tank reactors. This is a major component of the overall biodegradation process proposed for the complete mineralization of sulfur mustard. Several configurations were evaluated for degradation efficiency including batch, repeated batch, continuous stirred tank reactor (CSTR), and two-stage series CSTR. The repeated batch reactor provided the highest degradation rate of thiodiglycol. Further, this method degraded thiodiglycol in the liquid broth to below the detection limits (0.03 mM). Both batch and repeated batch experiments were simulated by an unstructured mathematical model. Simulation results were in agreement with the experimental data, particularly at low TDG concentration (around 30 mM). This study demonstrates the degradation of thiodiglycol using bioreactors and, more generally, is an experimental study of bioreactor designs for the degradation of growth-inhibitory substances.
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Affiliation(s)
- T Lee
- Center of Agricultural Biotechnology, University of Maryland and Biotechnology Institute, University of Maryland, College Park 20742, USA
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Pham MQ, Harvey SP, Weigand WA, Bentley WE. Reactor comparisons for the biodegradation of thiodiglycol, a product of mustard gas hydrolysis. Appl Biochem Biotechnol 1996; 57-58:779-89. [PMID: 8669917 DOI: 10.1007/bf02941758] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An environmentally benign method for the mineralization of sulfur mustard has been proposed involving chemical hydrolysis of sulfur mustard to thiodiglycol, and then the biological degradation of thiodiglycol to generate biomass and gaseous carbon dioxide. Alcaligenes xylosoxidans (SH91) was isolated based on its ability to utilize thiodiglycol as a sole carbon source. This article compares different biological reactor designs and experimentally assesses their relative effectiveness in degrading thiodiglycol using pure cultures of SH91. The reactor configurations studied are batch, continuous stirred-tank reactor (CSTR), and CSTR with cell recycle. From the results, it is clear that the CSTR with cell recycle offers superior performance for a given residence time or volume. These pure culture data are necessary for accurate design of a pilot-scale system where mixed cultures will be employed because of a possible incomplete chemical hydrolysis step.
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Affiliation(s)
- M Q Pham
- Department of Chemical Engineering, University of Maryland, College Park, USA
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