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Nguyen KQT, Nguyen HH, Phung HTT, Chung KL, Vu TY. A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers. J Biomol Struct Dyn 2024:1-8. [PMID: 38284361 DOI: 10.1080/07391102.2024.2308778] [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: 08/11/2023] [Accepted: 01/14/2024] [Indexed: 01/30/2024]
Abstract
PROTACs (Proteolysis Targeting Chimeras), heterobifunctional molecules, exhibit selectivity in degrading target proteins through E3 ubiquitin ligases. Designing effective PROTACs requires a deep understanding of the intricate binding interactions in the ternary complex (POI/PROTAC/E3 ligase), crucial for efficient target protein degradation. To address this challenge, we introduce a novel computational virtual screening method that considers essential amino acid interactions between the protein of interest and the chosen E3 ligase. This approach enhances accuracy and reliability, facilitating the strategic development of potent PROTACs. Utilizing a crystallized model of the VHL:PROTAC:SMARCA2BD ternary complex (PDB: 7Z6L), we assessed the effectiveness of our method. Our study reveals that increasing the number of essential restraints between the two proteins reduces the generated docking poses, leading to closer alignment with the experimental ternary complex. Specifically, utilizing three restraints showed the closest resemblance to the published complex, highlighting crucial interactions such as an H-bond between A:Gln 89 and B:Asn 67, along with two hydrophobic interactions: A:Gly 22 with B:Arg 69 and A:Glu 37 with B:Pro 99. This resulted in a significant decrease in the mean RMSD value from 31.8 and 31.0 Å to 24.4 Å, respectively. This underscores the importance of incorporating multiple essential restraints to enhance docking accuracy. Building on this progress, we introduce a systematic approach to design potential PROTACs between the Estrogen receptor and the E3 ligase, utilizing bridging intermediates with 4, 6, or 7 carbon atoms. By providing a more accurate and efficient means of identifying optimal PROTAC candidates, this approach has the potential to accelerate the development of targeted therapies and reduce the time and costs associated with drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Hieu Hien Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Khanh Linh Chung
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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2
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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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3
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Le HT, Tran LH, Phung HTT. SARS-CoV-2 omicron RBD forms a weaker binding affinity to hACE2 compared to Delta RBD in in-silico studies. J Biomol Struct Dyn 2023:1-10. [PMID: 37345564 DOI: 10.1080/07391102.2023.2222827] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
The COVID-19 pandemic sparked an unprecedented race in biotechnology in a search for effective therapies and a preventive vaccine. The continued appearance of SARS-CoV-2 variants of concern (VoCs) further swept the world. The entry of SARS-CoV-2 into cells is mediated by binding the receptor-binding domain (RBD) of the S protein to the cell-surface receptor, human angiotensin-converting enzyme 2 (hACE2). In this study, using a coarse-grained force field to parameterize the system, we employed steered-molecular dynamics (SMD) simulations to reveal the binding of SARS-CoV-2 Delta/Omicron RBD to hACE2. Our benchmarked results demonstrate a good correlation between computed rupture force and experimental binding free energy for known protein-protein systems. Moreover, our findings show that the Omicron RBD has a weaker binding affinity to hACE2, consistent with the respective experimental results. This indicates that our method can effectively be applied to other emerging SARS-CoV-2 strains.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hoa Thanh Le
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Linh Hoang Tran
- Faculty of Civil Engineering, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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4
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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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5
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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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Mai NT, Lan NT, Vu TY, Tung NT, Phung HTT. A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors. J Mol Model 2022; 28:163. [DOI: 10.1007/s00894-022-05149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/06/2022] [Indexed: 11/24/2022]
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Tran HT, Tran DH, Pham TNM, Phung HTT. DIRECT RECOMBINASE POLYMERASE AMPLIFICATION ASSAY FOR ACCURATE AND RAPID DETECTION OF LISTERIA MONOCYTOGENES IN FOOD. J microb biotech food sci 2022. [DOI: 10.55251/jmbfs.4749] [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: 11/19/2022] Open
Abstract
Listeria monocytogenes is one of the most common types of food poisoning bacteria which can cause serious foodborne diseases or even lethality. Generally, L. monocytogenes can be detected using traditional microbiology or molecular biology techniques, notably PCR. However, the application of these methods at the field is restricted due to the strict requirement of equipment and skilled personnel. In this study, recombinase polymerase amplification (RPA), an isothermal PCR assay was developed to rapidly detect L. monocytogenes in crude samples. The results showed that the RPA reaction, without requiring complex thermal cycles, was well-performed in the optimal conditions of 39°C within only 25 minutes. The limit of detection was identified as 310 fg of L. monocytogenes genomic DNA, which was 1000-fold more sensitive than the conventional PCR. RPA also succeeded to directly detect L. monocytogenes cells at a concentration as low as 2.5 × 101 Colony Forming Unit (CFU)/mL in pure cultures. In addition, RPA could accurately detect L. monocytogenes at 2.5 × 102 CFU/mL in milk without sample extraction or processing. Therefore, RPA established in this study could be an alternative standard method to confirm the presence of L. monocytogenes in food. Accordingly, this rapid and sensitive method could be further applied to clinical testing for the diagnosis of L. monocytogenes infection, especially in areas with limited settings.
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Tran DH, Tran HT, Pham TNM, Phung HTT. Direct multiplex recombinase polymerase amplification for rapid detection of S taphylococcus aureus and P seudomonas aeruginosa in food. Mol Biol Res Commun 2022; 11:1-10. [PMID: 35463821 PMCID: PMC9012432 DOI: 10.22099/mbrc.2021.41503.1664] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Food and beverage poisoning is detrimental to people's health since it can lead to fever, stomachaches, and even death. To rapidly detect the presence of foodborne pathogens, conventional PCR assays are currently widely employed. Meanwhile, isothermal PCR methods, in which the amplification reactions take place at a low and constant temperature, have lately emerged as effective and alternative means for quickly identifying pathogens in low-resource settings. Staphylococcus aureus and Pseudomonas aeruginosa are two of the most concerning foodborne bacterial infections. In this work, an isothermal PCR assay based on the Recombinase Polymerase Amplification (RPA) method was developed to simultaneously detect S. aureus and P. aeruginosa with high sensitivity and specificity. The limit of detection for multiplex RPA was 10 and 30 fg/reaction of S. aureus and P. aeruginosa genomic DNA, respectively. Furthermore, the reaction time was reduced to only 25 minutes, with a low incubation temperature of 39°C. Multiplex RPA reactions, in particular, were successful in directly identifying as low as 1 and 5 CFU/reaction of S. aureus and P. aeruginosa cells, respectively, without the need for DNA genome extraction. Moreover, the multiplex RPA reliably detected the two foodborne bacteria in milk, fruit juice, and bottled water samples. In conclusion, the direct multiplex RPA reported in this work offers a quick, easy, sensitive, and effective alternative approach for detecting the presence of S. aureus and P. aeruginosa without the requirement of a pricey instrument or highly-trained personnel.
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Affiliation(s)
| | | | | | - Huong Thi Thu Phung
- Corresponding Author: NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam. Tel: +84 981411701; Fax: +84 28 39 404 759 E. mail:
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9
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Bui LM, Thi Thu Phung H, Ho Thi TT, Singh V, Maurya R, Khambhati K, Wu CC, Uddin MJ, Trung DM, Chu DT. Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review. Bioengineered 2021; 12:8594-8613. [PMID: 34607509 PMCID: PMC8806999 DOI: 10.1080/21655979.2021.1987821] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
COVID-19 is one of the most severe global health crises that humanity has ever faced. Researchers have restlessly focused on developing solutions for monitoring and tracing the viral culprit, SARS-CoV-2, as vital steps to break the chain of infection. Even though biomedical engineering (BME) is considered a rising field of medical sciences, it has demonstrated its pivotal role in nurturing the maturation of COVID-19 diagnostic technologies. Within a very short period of time, BME research applied to COVID-19 diagnosis has advanced with ever-increasing knowledge and inventions, especially in adapting available virus detection technologies into clinical practice and exploiting the power of interdisciplinary research to design novel diagnostic tools or improve the detection efficiency. To assist the development of BME in COVID-19 diagnosis, this review highlights the most recent diagnostic approaches and evaluates the potential of each research direction in the context of the pandemic.
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Affiliation(s)
- Le Minh Bui
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.,Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Thuy-Tien Ho Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Mehsana, Gujarat, India
| | - Rupesh Maurya
- Department of Biosciences, School of Science, Indrashil University, Mehsana, Gujarat, India
| | - Khushal Khambhati
- Department of Biosciences, School of Science, Indrashil University, Mehsana, Gujarat, India
| | - Chia-Ching Wu
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Md Jamal Uddin
- ABEx Bio-Research Center, East Azampur, Dhaka, Bangladesh.,Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Republic of Korea
| | - Do Minh Trung
- Institute of Biomedicine and Pharmacy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Dinh Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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10
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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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11
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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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Ngo ST, Vu VV, Phung HTT. Computational investigation of possible inhibitors of the winged-helix domain of MUS81. J Mol Graph Model 2020; 103:107771. [PMID: 33340918 DOI: 10.1016/j.jmgm.2020.107771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/17/2020] [Revised: 09/09/2020] [Accepted: 09/28/2020] [Indexed: 01/01/2023]
Abstract
The methyl methanesulfonate and ultraviolet sensitive 81 (MUS81) is a structure-specific endonuclease that is highly conserved in eukaryotes and essential for homologous recombination repair. The winged-helix domain at the N-terminus of MUS81 (wMUS81) can bind DNA substrates and regulate the endonuclease activity. The repression of MUS81 activity could enhance the sensitivity to antitumor compounds of different tumour cells. Thus, MUS81 is a potential therapeutic target in cancer therapy. However, specific inhibitors of MUS81 have remained elusive. Here, for the first time, we attempt to discover the compounds disrupting the wMUS81 activity. The binding affinity of available drugs to wMUS81 was first estimated by molecular docking. pKa values were taken into consideration to eliminate unlikely protonation states of the ligands. Top-lead compounds were then estimated the binding affinity using the fast pulling ligand simulations. Finally, the free energy perturbation method accurately defined the absolute binding free energy of the top four ligands, revealing the most potential inhibitors of wMUS81 including simeprevir and nilotinib. Binding of simeprevir destabilizes the β-hairpin region of wMUS81, likely disturbing the wMUS81 function. The van der Waals free binding energy majorly modulates the ligand-binding mechanism. The two conserved residues Leu189 and Arg196 are likely important in monitoring the interacting process of simeprevir to wMUS81.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, 700000, Viet Nam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, 700000, Viet Nam.
| | - Van Van Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, 700000, Viet Nam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, 700000, Viet Nam.
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13
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Mai NT, Lan NT, Vu TY, Duong PTM, Tung NT, Phung HTT. Corrigendum to 'Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations'. J Mol Graph Model 2020; 103:107805. [PMID: 33246192 DOI: 10.1016/j.jmgm.2020.107805] [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: 11/19/2022]
Affiliation(s)
- Nguyen Thi Mai
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Viet Nam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Ngo Thi Lan
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Phuong Thi Mai Duong
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
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Tran DH, Tran HT, Le UP, Vu XD, Trinh TBN, Do HDK, Than VT, Bui LM, Vu VV, Nguyen TL, Phung HTT, Le VP. Direct colorimetric LAMP assay for rapid detection of African swine fever virus: A validation study during an outbreak in Vietnam. Transbound Emerg Dis 2020; 68:2595-2602. [PMID: 33064865 DOI: 10.1111/tbed.13879] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022]
Abstract
African swine fever (ASF) is a highly infectious viral disease with high mortality. The most recent ASF outbreak in Vietnam began in 2019, posing a threat to spread to the neighbouring Asian countries. Without a commercial vaccine or efficient chemotherapeutics, rapid diagnosis and necessary biosecurity procedures are required to control the disease. While the diagnostic method of ASF recommended by the World Organization of Animal Health is real-time PCR, the ideal diagnosis procedure including master mix setup, template extraction and a high-cost qPCR equipment for many samples being tested simultaneously is not portable. In this study, a colorimetric loop-mediated isothermal amplification (LAMP) assay was modified and evaluated for ASF virus detection using crude serum samples collected from domestic pigs in Vietnam during the 2019 outbreak. The LAMP results can be readily visualized to the naked eye within 30 min without the requirement of DNA extraction and sophisticated equipment. The sensitivity, specificity and limit of detection of direct colorimetric LAMP assay were comparable to a commercial diagnostic real-time PCR kit. Results strongly indicate that the adapted colorimetric LAMP assay has a remarkable potential for the in-field diagnosis of ASF.
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Affiliation(s)
- Diem Hong Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hau Thi Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Uyen Phuong Le
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Xuan Dang Vu
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Thi Bich Ngoc Trinh
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Van Thai Than
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi, Vietnam.,A&A Green Phoenix Group, Phenikaa Research and Technology Institute (PRATI), Hanoi, Vietnam
| | - Le Minh Bui
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Van Van Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Thi Lan Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Van Phan Le
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
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15
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Phung HTT, Tran DH, Nguyen TX. The cruciform DNA-binding protein Crp1 stimulates the endonuclease activity of Mus81-Mms4 in Saccharomyces cerevisiae. FEBS Lett 2020; 594:4320-4337. [PMID: 32936932 DOI: 10.1002/1873-3468.13931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/21/2020] [Revised: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 11/07/2022]
Abstract
The Saccharomyces cerevisiae Mus81-Mms4 complex is a highly conserved DNA structure-specific endonuclease that plays essential roles in the processing of recombination intermediates that arise during the repair of stalled replication forks and double-stranded breaks. To identify novel factors functioning conjointly with Mus81-Mms4, we performed a biochemical screen and found that Crp1, a cruciform DNA-recognizing protein that specifically binds to DNA four-way junction structures, could stimulate the Mus81-Mms4 endonuclease. The specific protein interaction between Mus81-Mms4 and Crp1 was responsible for the stimulation observed. Multicopy expression of Crp1 could partially rescue the sensitivity to DNA-damaging agents of the sgs1∆mus81∆21-24N mutant. Our results provide insight into the functional role and interaction of Crp1 with other proteins involved in DNA repair.
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Affiliation(s)
- Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Diem Hong Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Ta Xuan Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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16
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Mai NT, Lan NT, Vu TY, Duong PTM, Tung NT, Phung HTT. Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations. J Mol Graph Model 2020; 100:107648. [PMID: 32653524 DOI: 10.1016/j.jmgm.2020.107648] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 02/02/2020] [Revised: 04/29/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Checkpoint kinase 1 (CHK1) is a serine/threonine-protein kinase that is involved in cell cycle regulation in eukaryotes. Inhibition of CHK1 is thus considered as a promising approach in cancer therapy. In this study, the fast pulling of ligand (FPL) process was applied to predict the relative binding affinities of CHK1 inhibitors using non-equilibrium molecular dynamics (MD) simulations. The work of external harmonic forces to pull the ligand out of the binding cavity strongly correlated with the experimental binding affinity of CHK1 inhibitors with the correlation coefficient of R = -0.88 and an overall root mean square error (RMSE) of 0.99 kcal/mol. The data indicate that the FPL method is highly accurate in predicting the relative binding free energies of CHK1 inhibitors with an affordable CPU time. A new set of molecules were designed based on the molecular modeling of interactions between the known inhibitor and CHK1 as inhibitory candidates. Molecular docking and FPL results exhibited that the binding affinities of developed ligands were similar to the known inhibitor in interaction with the catalytic site of CHK1, producing very potential CHK1 inhibitors of that the inhibitory activities should be further evaluated in vitro.
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Affiliation(s)
- Nguyen Thi Mai
- Laboratory of Theoretical and Computational Biophysics, Ho Chi Minh City, Viet Nam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Ngo Thi Lan
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam
| | - Thien Y Vu
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - Phuong Thi Mai Duong
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology, Academy of Science and Technology, Hanoi, Viet Nam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
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17
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Tran DH, Phung HTT. Detecting Fasciola hepatica and Fasciola gigantica microRNAs with loop-mediated isothermal amplification (LAMP). J Parasit Dis 2019; 44:364-373. [PMID: 32508411 DOI: 10.1007/s12639-019-01164-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 06/21/2019] [Accepted: 09/25/2019] [Indexed: 12/28/2022] Open
Abstract
Fascioliasis is a parasitic infection typically caused by two common parasites of class Trematodo, genus Fasciola, namely Fasciola hepatica and Fasciola gigantica. The widespread of these species in water and food makes fascioliasis become a global zoonotic disease that affects 2.4 million people in more than 75 countries worldwide. Typically, F. hepatica and F. gigantica can be recognized by parasitological techniques to detect Fasciola spp. eggs, immunological techniques to detect worm-specific antibodies, or by molecular techniques such as PCR to detect parasitic genomic DNA. Recently, miRNAs have been raised as a key regulator and potential diagnostic biomarkers of diseases, including parasitic infection. An isothermal PCR called loop-mediated isothermal amplification (LAMP) is rapid, sensitive, and its amplification process is so extensive that making LAMP well-suited for field diagnostics. LAMP reactions for miRNA detection have been introduced and were able to detect the target miRNA amounts in the wide range of 1.0 amol to 1.0 pmol, exhibiting high selectivity to differentiate one-base between miRNA sequences. Here, we introduced a modified LAMP to detect a species-specific miRNA of F. hepatica and F. gigantica. Our method did not demand an initial heating step and the reactions had a high sensitivity that greater than 1000 times in comparison to that reported in previous studies. Most importantly, the technique could perform well with parasitic miRNA presenting in bovine serum samples without sophisticated equipment required. These results create a promising technique basis for some novel and simple device to diagnose fascioliasis and other parasitic infection diseases at point-of-care.
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Affiliation(s)
- Diem Hong Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ward 13, District 4, Ho Chi Minh City, 700000 Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ward 13, District 4, Ho Chi Minh City, 700000 Vietnam
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18
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Ngo ST, Tran-Le PD, Ho GT, Le LQ, Bui LM, Vu BK, Thu Phung HT, Nguyen HD, Vo TS, Vu VV. Interaction of carbohydrate binding module 20 with starch substrates. RSC Adv 2019; 9:24833-24842. [PMID: 35528656 PMCID: PMC9069913 DOI: 10.1039/c9ra01981b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 03/14/2019] [Accepted: 07/23/2019] [Indexed: 12/03/2022] Open
Abstract
CBM20s are starch-binding domains found in many amylolytic enzymes, including glucoamylase, alpha-amylase, beta-amylases, and a new family of starch-active polysaccharide monooxygenases (AA13 PMOs). Previous studies of CBM20–substrate interaction only concerned relatively small or soluble amylose molecules, while amylolytic enzymes often work on extended chains of insoluble starch molecules. In this study, we utilized molecular simulation techniques to gain further insights into the interaction of CBM20 with substrates of various sizes via its two separate binding sites, termed as BdS1 and BdS2. Results show that substrate binding at BdS1 involving two conserved tryptophan residues is about 2–4 kcal mol−1 stronger than that at BdS2. CBM20 exhibits about two-fold higher affinity for helical substrates than for the amylose random coils. The affinity for amylose individual double helices does not depend on the helices' length. At least three parallel double helices are required for optimal binding. The binding affinity for a substrate containing 3 or more double helices is ∼−15 kcal mol−1, which is 2–3 kcal mol−1 larger than that for individual double helices. 100 ns molecular dynamics simulations were carried out for the binding of CBM20 to an extended substrate containing 3 layers of 9 60-unit double helices (A3L). A stable conformation of CBM20–A3L was found at BdS1. However, when CBM20 binds A3L viaBdS2, it moves across the surface of the substrate and does not form a stable complex. MD simulations show that small amylose helices are quickly disrupted upon binding to CBM20. Our results provide some important molecular insights into the interactions of CBM20 with starch substrates, which will serve as the basis for further studies of CBM20-containing enzymes, including AA13 PMOs. CBM20 quickly disrupts small helical amylose substrates and exhibits optimal binding affinity when the substrate has three or more parallel double helices.![]()
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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
| | | | - Giap T. Ho
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Loan Q. Le
- Institute of Tropical Biology
- Vietnam Academy of Science and Technology
- Ho Chi Minh City
- Vietnam
| | - Le Minh Bui
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Bao Khanh Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | | | - Hoang-Dung Nguyen
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
- Institute of Tropical Biology
| | - Thanh-Sang Vo
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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19
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Phung HTT, Nguyen HLH, Vo ST, Nguyen DH, Le MV. Saccharomyces cerevisiae Mus81-Mms4 and Rad52 can cooperate in the resolution of recombination intermediates. Yeast 2018; 35:543-553. [PMID: 29738624 DOI: 10.1002/yea.3320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 10/09/2017] [Revised: 02/26/2018] [Accepted: 04/23/2018] [Indexed: 11/06/2022] Open
Abstract
Mus81 is a well-conserved DNA structure-specific endonuclease which belongs to the XPF/Rad1 family of proteins that are involved in DNA nucleotide excision repair. Mus81 forms a heterodimer with a non-catalytic subunit, Mms4, in Saccharomyces cerevisiae (Eme1/EME1 in Schizosaccharomyces pombe and mammals). Recent evidence shows that Mus81 functions redundantly with Sgs1, a member of the ubiquitous RecQ family of DNA helicases, to process toxic recombinant intermediates. In budding yeast, homologous recombination is regulated by the Rad52 epistasis group of proteins, including Rad52, which stimulates the main steps of DNA sequence-homology searching. Mus81 was proven to act in the Rad52-dependent pathway. Here, we demonstrate that Rad52 and Mus81-Mms4 possesses a functional interaction; the presence of Rad52 significantly enhances the endonuclease activity of Mus81-Mms4 on a broad range of its preferred synthetic substrates. Furthermore, this functional interaction is demonstrated to be species specific. We fragmented Rad52 and found that the N-terminal fragment from the 86th to 169th amino acid residue, which belongs to DNA-binding and self-association domains, can stimulate Mus81-Mms4 endonuclease. These results strongly support the notion that Rad52 and Mus81-Mms4 collaborate and work jointly in processing of homologous recombination intermediates.
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Affiliation(s)
- Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ward 13, District 4, Ho Chi Minh city, 700000, Vietnam
| | - Hoa Luong Hieu Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ward 13, District 4, Ho Chi Minh city, 700000, Vietnam
| | - Sang Thanh Vo
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ward 13, District 4, Ho Chi Minh city, 700000, Vietnam
| | - Dung Hoang Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ward 13, District 4, Ho Chi Minh city, 700000, Vietnam
| | - Minh Van Le
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ward 13, District 4, Ho Chi Minh city, 700000, Vietnam
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20
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Phung HTT, Nguyen HLH, Nguyen DH. The possible function of Flp1 in homologous recombination repair in Saccharomyces cerevisiae. AIMS Genet 2018; 5:161-176. [PMID: 31435519 PMCID: PMC6698574 DOI: 10.3934/genet.2018.2.161] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/18/2018] [Indexed: 11/18/2022]
Abstract
Saccharomyces cerevisiae Mus81 is a structure-selective endonuclease which constitutes an alternative pathway in parallel with the helicase-topoisomerase Sgs1-Top3-Rmi1 complex to resolve a number of DNA intermediates during DNA replication, repair, and homologous recombination. Previously, it was showed that the N-terminal region of Mus81 was required for its in vivo function in a redundant manner with Sgs1; mus81Δ120N mutant that lacks the first 120 amino acid residues at the N-terminus exhibited synthetic lethality in combination with the loss of SGS1. In this study, the physiologically important role of the N-terminal region of Mus81 in processing toxic intermediates was further investigated. We examined the cellular defect of sgs1Δmus81Δ100N cells and observed that although viable, the cells became very sensitive to DNA damaging agents. A single-copy suppressor screening to seek for a factor(s) that could rescue the drug sensitivity of sgs1Δmus81Δ100N cells was performed and revealed that Flp1, a site-specific recombinase 1 encoded on the 2-micron plasmid was a suppressor. Moreover, Flp1 overexpression could partially suppress the drug sensitivity of mus81Δ cells at 37 °C. Our findings suggest a possible function of Flp1 in coordination with Mus81 and Sgs1 to jointly resolve the branched-DNA structures generated in cells attempting to repair DNA damages.
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Affiliation(s)
- Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh city, Vietnam
| | | | - Dung Hoang Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh city, Vietnam
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21
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Ngo ST, Thu Phung HT, Vu KB, Vu VV. Atomistic investigation of an Iowa Amyloid-β trimer in aqueous solution. RSC Adv 2018; 8:41705-41712. [PMID: 35558787 PMCID: PMC9091969 DOI: 10.1039/c8ra07615d] [Citation(s) in RCA: 8] [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: 09/13/2018] [Accepted: 12/04/2018] [Indexed: 11/21/2022] Open
Abstract
The self-assembly of Amyloid beta (Aβ) peptides are widely accepted to associate with Alzheimer's disease (AD) via several proposed mechanisms. Because Aβ oligomers exist in a complicated environment consisting of various forms of Aβ, including oligomers, protofibrils, and fibrils, their structure has not been well understood. The negatively charged residue D23 is one of the critical residues of the Aβ peptide as it is located in the central hydrophobic domain of the Aβ N-terminal and forms a salt-bridge D23-K28, which helps stabilize the loop domain. In the familial Iowa (D23N) mutant, the total net charge of Aβ oligomers decreases, resulting in the decrease of electrostatic repulsion between D23N Aβ monomers and thus the increase in their self-aggregation rate. In this work, the impact of the D23N mutation on 3Aβ11–40 trimer was characterized utilizing temperature replica exchange molecular dynamics (REMD) simulations. Our simulation reveals that D23N mutation significantly enhances the affinity between the constituting chains in the trimer, increases the β-content (especially in the sequence 21–23), and shifts the β-strand hydrophobic core from crossing arrangement to parallel arrangement, which is consistent with the increase in self-aggregation rate. Molecular docking indicates that the Aβ fibril-binding ligands bind to the D23N and WT forms at different poses. These compounds prefer to bind to the N-terminal β-strand of the D23N mutant trimer, while they mostly bind to the N-terminal loop region of the WT. It is important to take into account the difference in the binding of ligands to mutant and wild type Aβ peptides in designing efficient inhibitors for various types of AD. Amyloid beta peptide oligomers are believed to play key roles in Alzheimer's disease pathogenesis. D23N mutation significantly changes their structure and how they bind potential inhibitors.![]()
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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
| | | | - Khanh B. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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22
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Nakamura M, Tohya Y, Miyazawa T, Mochizuki M, Phung HTT, Nguyen NH, Huynh LMT, Nguyen LT, Nguyen PN, Nguyen PV, Nguyen NPT, Akashi H. A novel antigenic variant of Canine parvovirus from a Vietnamese dog. Arch Virol 2004; 149:2261-9. [PMID: 15503211 DOI: 10.1007/s00705-004-0367-y] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [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: 02/09/2004] [Accepted: 04/29/2004] [Indexed: 10/26/2022]
Abstract
Nine isolates of Canine parvovirus (CPV) were obtained from Vietnamese dogs and cats. One canine isolate showed a unique antigenic property which indicates a novel antigenic variant of CPV-2b when examined with hemagglutination inhibition tests using our monoclonal antibodies, 21C3 and 19D7, which were recently developed. This isolate had an amino acid substitution of residue 426, Asp to Glu, and the same substitution has recently been found in CPV from Italian dogs. This study first showed that such substitution caused an antigenic difference demonstrable by monoclonal antibodies and that a similar evolution may have occurred in CPV in Vietnam.
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Affiliation(s)
- M Nakamura
- Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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