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Panda SK, Karmakar S, Sen Gupta PS, Rana MK. Can Duvelisib and Eganelisib work for both cancer and COVID-19? Molecular-level insights from MD simulations and enhanced samplings. Phys Chem Chem Phys 2024; 26:10961-10973. [PMID: 38526354 DOI: 10.1039/d3cp05934k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
SARS-CoV-2 has caused severe illness and anxiety worldwide, evolving into more dreadful variants capable of evading the host's immunity. Cytokine storms, led by PI3Kγ, are common in cancer and SARS-CoV-2. Naturally, there is a yearning to see whether any drugs could alleviate cytokine storms for both. Upon investigation, we identified two anticancer drugs, Duvelisib and Eganelisib, that could also work against SARS-CoV-2. This report is the first to decipher their synergic therapeutic effectiveness against COVID-19 and cancer with molecular insights from atomistic simulations. In addition to PI3Kγ, these drugs exhibit specificity for the main protease among all SARS-CoV-2 targets, with significant negative binding free energies and small time-dependent conformational changes of the complexes. Complexation makes active sites and secondary structures highly mechanically stiff, with barely any deformation. Replica simulations estimated large pulling forces in enhanced sampling to dissociate the drugs from Mpro's active site. Furthermore, the radial distribution function (RDF) demonstrated that the therapeutic molecules were closest to the His41 and Cys145 catalytic dyad residues. Finally, analyses implied Duvelisib and Eganelisib as promising dual-purposed anti-COVID and anticancer drugs, potentially targeting Mpro and PI3Kγ to stop virus replication and cytokine storms concomitantly. We also distinguished hotspot residues imparting significant interactions.
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Affiliation(s)
- Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Shaswata Karmakar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
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2
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Lalithamaheswari B, Anu Radha C. Structural and binding studies of 2'- and 3-fucosyllactose and its complexes with norovirus capsid protein by molecular dynamics simulations. J Biomol Struct Dyn 2023; 41:10230-10243. [PMID: 36476051 DOI: 10.1080/07391102.2022.2153923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Human breast milk contains free oligosaccharides (Human Milk Oligosaccharides-HMOs) that help to protect breastfed infants against a variety of infectious diseases and act as decoy receptors. In breast milk, HMOs are the third most abundant compounds after lactose and lipids. Structural and conformational models of HMOs are quite crucial to studying the interaction with proteins and molecular recognition phenomenon. Molecular dynamics simulations for two trisaccharides HMOs (2'-FL and 3-FL) were carried out for 250 ns and the conformational models were subsequently substantiated by three replicate simulations. The conformer models of HMOs 2'-FL and 3-FL were deposited in the 3-Dimensional Structural Database for Sialic acid-containing CARbohydrates (3DSDSCAR) database website (www.3dsdscar.in). HMOs were then docked into the active site of norovirus capsid protein and are simulated for 100 ns duration. Each complex system was stabilized by direct and water-mediated hydrogen bonding interactions. Binding free energy calculations predict two possible binding modes for each complex system. The conformational flexibility and binding stability of the complex systems were calculated. The protein folding/unfolding and compactness seem to be better for the two HMOs. From a general perspective, we found that both 2'-FL and 3-FL exhibited higher binding efficacy towards norovirus capsid protein and according to the structural stability, 3-FL might be used as a preventive inhibitor for norovirus infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Lalithamaheswari
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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3
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Kurt M, Ercan S, Pirinccioglu N. Designing new drug candidates as inhibitors against wild and mutant type neuraminidases: molecular docking, molecular dynamics and binding free energy calculations. J Biomol Struct Dyn 2023; 41:7847-7861. [PMID: 36152997 DOI: 10.1080/07391102.2022.2125440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
Influenza virus is the cause of the death of millions of people with about 3-4 pandemics every hundred years in history. It also turns into a seasonal disease, bringing about approximately 5-15% of the population to be infected and 290,000-650,000 people to die every year. These numbers reveal that it is necessary to be on the alert to work towards influenza in order to protect public health. There are FDA-approved antiviral drugs such as oseltamivir and zanamivir recommended by the World Center for Disease Prevention. However, after the recent outbreaks such as bird flu and swine flu, increasing studies have shown that the flu virus has gained resistance to these drugs. So, there is an urgent need to find new drugs effective against this virus. This study aims to investigate new drug candidates targeting neuraminidase (NA) for the treatment of influenza by using computer aided drug design approaches. They involve virtual scanning, de novo design, rational design, docking, MD, MMGB/PBSA. The investigation includes H1N1, H5N1, H2N2 and H3N2 neuraminidase proteins and their mutant variants possessing resistance to FDA-approved drugs. Virtual screening consists of approximately 30 thousand molecules while de novo and rational designs produced over a hundred molecules. These approaches produced three lead molecules with binding energies for both non-mutant (-34.84, -59.99 and -60.66 kcal/mol) and mutant (-40.40, -58.93, -76.19 kcal/mol) H2N2 NA calculated by MM-PBSA compared with those of oseltamivir -25.64 and -18.40 respectively. The results offer new drug candidates against influenza infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Murat Kurt
- Institute of Science, Dicle University, Diyarbakır, Turkey
| | - Selami Ercan
- Department of Chemistry, Batman University, Batman, Turkey
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4
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Yadav M, Igarashi M, Yamamoto N. Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. PeerJ 2021; 9:e11552. [PMID: 34141489 PMCID: PMC8179223 DOI: 10.7717/peerj.11552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/11/2021] [Indexed: 12/11/2022] Open
Abstract
Background Oseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated. Methods In this study, we used dynamic residue interaction network (dRIN) analysis based on molecular dynamics simulation to investigate the correlation between the OTV binding site of NA and its H274Y mutation site. Results dRIN analysis revealed that the OTV binding site and H274Y mutation site of NA interact via the three interface residues connecting them. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, thereby significantly decreasing the interaction between OTV and its surrounding loop 150 residues. Thus, we concluded that such changes in residue interactions could reduce the binding affinity of OTV to NA, resulting in drug resistant influenza viruses. Using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions due to H274Y mutation, which can elucidate the molecular mechanism of reduction in OTV binding affinity to influenza NA. Finally, the dRIN analysis used in this study can be widely applied to various systems such as individual proteins, protein-ligand complexes, and protein-protein complexes, to characterize the dynamic aspects of the interactions.
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Affiliation(s)
- Mohini Yadav
- Department of Applied Chemistry, Faculty of Engineering, Chiba Institute of Technology, Narashino, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Norifumi Yamamoto
- Department of Applied Chemistry, Faculty of Engineering, Chiba Institute of Technology, Narashino, Japan
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5
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Nguyen H, Thai NQ, Truong DT, Li MS. Remdesivir Strongly Binds to Both RNA-Dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations. J Phys Chem B 2020; 124:11337-11348. [PMID: 33264025 PMCID: PMC7724981 DOI: 10.1021/acs.jpcb.0c07312] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/12/2020] [Indexed: 02/07/2023]
Abstract
The outbreak of a new coronavirus SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) has caused a global COVID-19 (coronavirus disease 2019) pandemic, resulting in millions of infections and thousands of deaths around the world. There is currently no drug or vaccine for COVID-19, but it has been revealed that some commercially available drugs are promising, at least for treating symptoms. Among them, remdesivir, which can block the activity of RNA-dependent RNA polymerase (RdRp) in old SARS-CoV and MERS-CoV viruses, has been prescribed to COVID-19 patients in many countries. A recent experiment showed that remdesivir binds to SARS-CoV-2 with an inhibition constant of μM, but the exact target has not been reported. In this work, combining molecular docking, steered molecular dynamics, and umbrella sampling, we examined its binding affinity to two targets including the main protease (Mpro), also known as 3C-like protease, and RdRp. We showed that remdesivir binds to Mpro slightly weaker than to RdRp, and the corresponding inhibition constants, consistent with the experiment, fall to the μM range. The binding mechanisms of remdesivir to two targets differ in that the electrostatic interaction is the main force in stabilizing the RdRp-remdesivir complex, while the van der Waals interaction dominates in the Mpro-remdesivir case. Our result indicates that remdesivir can target not only RdRp but also Mpro, which can be invoked to explain why this drug is effective in treating COVID-19. We have identified residues of the target protein that make the most important contribution to binding affinity, and this information is useful for drug development for this disease.
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Affiliation(s)
- Hoang
Linh Nguyen
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Quoc Thai
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City 870000, Dong Thap, Vietnam
| | - Duc Toan Truong
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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6
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Abstract
![]()
Accurate determination
of the binding affinity of the ligand to
the receptor remains a difficult problem in computer-aided drug design.
Here, we study and compare the efficiency of Jarzynski’s equality
(JE) combined with steered molecular dynamics and the linear interaction
energy (LIE) method by assessing the binding affinity of 23 small
compounds to six receptors, including β-lactamase, thrombin,
factor Xa, HIV-1 protease (HIV), myeloid cell leukemia-1, and cyclin-dependent
kinase 2 proteins. It was shown that Jarzynski’s nonequilibrium
binding free energy ΔGneqJar correlates with the available
experimental data with the correlation levels R =
0.89, 0.86, 0.83, 0.80, 0.83, and 0.81 for six data sets, while for
the binding free energy ΔGLIE obtained
by the LIE method, we have R = 0.73, 0.80, 0.42,
0.23, 0.85, and 0.01. Therefore, JE is recommended to be used for
ranking binding affinities as it provides accurate and robust results.
In contrast, LIE is not as reliable as JE, and it should be used with
caution, especially when it comes to new systems.
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Affiliation(s)
- Kiet Ho
- Institute for Computational Sciences and Technology, Quang Trung Software City, SBI Building, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Duc Toan Truong
- Institute for Computational Sciences and Technology, Quang Trung Software City, SBI Building, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Department of Theoretical Physics, Faculty of Physics and Engineering Physics, Ho Chi Minh University of Science, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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7
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Gancar M, Ho K, Mohid SA, Thai NQ, Bednarikova Z, Nguyen HL, Bhunia A, Nepovimova E, Li MS, Gazova Z. 7-Methoxytacrine and 2-Aminobenzothiazole Heterodimers: Structure-Mechanism Relationship of Amyloid Inhibitors Based on Rational Design. ACS Chem Neurosci 2020; 11:715-729. [PMID: 32011847 DOI: 10.1021/acschemneuro.9b00419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The formation and accumulation of amyloid aggregates are the phenomena that accompany amyloidoses, which are currently untreatable and include Alzheimer's and Parkinson's diseases, diabetes mellitus, non-neuropathic lysozyme systemic amyloidosis, and others. One of the very promising therapeutic approaches seems to be an inhibition of amyloid formation and/or clearance of amyloid aggregates. Small molecules have a great potential to interfere with amyloid fibrillation of peptides and polypeptides, which can be improved by connection of cyclic structures into single multicyclic molecules and their dimerization. In our study, we focused on heterodimers consisting of 7-methoxytacrine (7-MEOTA) and 2-aminobenzothiazole (BTZ) parent molecules connected by an aliphatic linker. Using in vitro and in silico methods, we investigated the ability of studied compounds to inhibit the amyloid aggregation of hen egg white lysozyme. Heterodimerization led to significant improvement of inhibitory activity compared to that of the parent molecules. The efficiency of the heterodimers varied; the most effective inhibitor contained the longest linker, eight carbons long. We suggest that binding of a heterodimer to a lysozyme blocks the interaction between the β-domain and C-helix region essential for the formation of amyloid cross-β structure. Elongation of the linker ultimately enhances the compound's ability to prevent this interaction by allowing the BTZ part of the heterodimer to bind more effectively, increasing the compound's binding affinity, and also by greater steric obstruction. This study represents an important contribution to the recent rational design of potential lead small molecules with anti-amyloid properties, and the heterodimers studied are prospective candidates for the treatment of systemic lysozyme amyloidosis and other amyloid-related diseases.
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Affiliation(s)
- Miroslav Gancar
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Kiet Ho
- Life Science Lab, Institute of Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Sk. Abdul Mohid
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, Ghose Bagan, CIT Road Scheme VIIM, West Bengal 700054, Kolkata, India
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City 700000, Dong Thap, Vietnam
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - H. Linh Nguyen
- Life Science Lab, Institute of Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, Ghose Bagan, CIT Road Scheme VIIM, West Bengal 700054, Kolkata, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
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8
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Ngo ST, Mai BK, Derreumaux P, Vu VV. Adequate prediction for inhibitor affinity of Aβ 40 protofibril using the linear interaction energy method. RSC Adv 2019; 9:12455-12461. [PMID: 35515829 PMCID: PMC9063661 DOI: 10.1039/c9ra01177c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 11/21/2022] Open
Abstract
The search for efficient inhibitors targeting Aβ oligomers and fibrils is an important issue in Alzheimer's disease treatment. As a consequence, an accurate and computationally cheap approach to estimate the binding affinity for many ligands interacting with Aβ peptides is very important. Here, the calculated binding free energies of 30 ligands interacting with 12Aβ11-40 peptides using the linear interaction energy (LIE) approach are found to be in good correlation with experimental data (R = 0.79). The binding affinities of these complexes are also calculated by using free energy perturbation (FEP) and molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) methods. The time-consuming FEP method provides results with similar correlation (R = 0.72), whereas MM/PBSA calculations show very low correlation with experimental data (R = 0.27). In all complexes, van der Waals interactions contribute much more than electrostatic interactions. The LIE model, which is much less time-consuming than both the FEP and MM/PBSA methods, opens the door to accurate and rapid affinity prediction of ligands with Aβ peptides and the design of new ligands.
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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
| | - Binh Khanh Mai
- Institute for Computational Science and Technology (ICST), Quang Trung Software City Ho Chi Minh City Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot 13 rue Pierre et Marie Curie 75005 Paris France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Pharmacy, Ton Duc Thang 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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9
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Thai NQ, Bednarikova Z, Gancar M, Linh HQ, Hu CK, Li MS, Gazova Z. Compound CID 9998128 Is a Potential Multitarget Drug for Alzheimer's Disease. ACS Chem Neurosci 2018; 9:2588-2598. [PMID: 29775277 DOI: 10.1021/acschemneuro.8b00091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We have probed small molecule compound CID 9998128 as a potential multitarget drug for the Alzheimer's disease (AD) using in silico and in vitro experiments. By all-atom simulation and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, we have demonstrated that this compound strongly binds to both amyloid β42 (Aβ42) fibrils and β-secretase, and the van der Waals interaction dominates over the electrostatic interaction in binding affinity. A detailed analysis at the atomic level revealed that indazole in CID 99998128 structure made a major contribution to instability of all studied complexes. In vitro experiments have shown that CID 9998128 inhibits the Aβ42 amyloid fibrillization and is capable to clear Aβ42 fibrils. Moreover, the compound dose-dependently decreases β-site amyloid precursor protein cleaving enzyme (BACE-1) activity with EC50 value in micromolar range. Thus, our study has revealed that CID 9998128 is a good candidate for AD treatment through preventing production of Aβ peptides and degrading their aggregates. For drug design, we predict that the chemical structure of potent AD multitarget inhibitors should not contain indazole.
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Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Sciences and Technology, SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Vietnam
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, Kosice 040 01, Slovakia
| | - Miroslav Gancar
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, Kosice 040 01, Slovakia
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Vietnam
| | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
- Physics Division, National Center for Theretical Sciences, Hsinchu 30013, Taiwan
- Department of Physics, National Dong Hwa University, Hualien 97401, Taiwan
- Department of Systems Science, University of Schanghai for Science and Technology, Shanghai 200093, China
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, Kosice 040 01, Slovakia
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10
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Nguyen H, Pham T, Nguyen HL, Phan T. Investigation of Binding Affinity Between Prokaryotic Proteins (AHU-IHF) and DNAs: Steered Molecular Dynamics Approach. Appl Biochem Biotechnol 2018; 186:834-846. [DOI: 10.1007/s12010-018-2735-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/12/2018] [Indexed: 11/29/2022]
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11
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Ouyang Y, Zhao L, Zhang Z. Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00067k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The conformations of p53 TAD2 in complexes and sampled in simulations with five force fields.
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Affiliation(s)
- Yanhua Ouyang
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
| | - Likun Zhao
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
| | - Zhuqing Zhang
- College of Life Science, University of Chinese Academy of Sciences
- Beijing
- China
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12
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Pham HDQ, Thai NQ, Bednarikova Z, Linh HQ, Gazova Z, Li MS. Bexarotene cannot reduce amyloid beta plaques through inhibition of production of amyloid beta peptides:in silicoandin vitrostudy. Phys Chem Chem Phys 2018; 20:24329-24338. [DOI: 10.1039/c8cp00049b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recently, it has been reported that anti-cancer drug bexarotene can remarkably destroy amyloid beta (Aβ) plaques in mouse models suggesting therapeutic potential for Alzheimer's disease.
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Affiliation(s)
- Huy Dinh Quoc Pham
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute for Computational Science and Technology
| | - Nguyen Quoc Thai
- Institute for Computational Science and Technology
- Quang Trung Software City
- Ho Chi Minh City
- Vietnam
- Biomedical Engineering Department
| | - Zuzana Bednarikova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
| | - Huynh Quang Linh
- Biomedical Engineering Department
- University of Technology
- Ho Chi Minh City
- Vietnam
| | - Zuzana Gazova
- Department of Biophysics
- Institute of Experimental Physics
- Slovak Academy of Sciences
- 040 01 Kosice
- Slovakia
| | - Mai Suan Li
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
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13
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Huy PDQ, Thai NQ, Bednarikova Z, Phuc LH, Linh HQ, Gazova Z, Li MS. Bexarotene Does Not Clear Amyloid Beta Plaques but Delays Fibril Growth: Molecular Mechanisms. ACS Chem Neurosci 2017; 8:1960-1969. [PMID: 28689412 DOI: 10.1021/acschemneuro.7b00107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In 2012, it was reported that anticancer drug bexarotene reduced amyloid plaque and improved mental functioning in a small sample of mice engineered to exhibit Alzheimer's like symptoms. It has been suggested that bexarotene stimulates expression of apolipoprotein E (ApoE) leading to intracellular clearance of amyloid beta (Aβ). However, the effect of bexarotene on clearance of plaques has not been seen in some mouse models. Two interesting questions include whether bexarotene can destroy Aβ fibrils via direct interaction with them and how this compound impacts the lag phase in the fibril growth process. By the Thioflavin T fluorescence assay and atomic force microscopy, we have shown that bexarotene prolongs the lag phase, but it does not degrade Aβ fibrils. The impotence of bexarotene in destroying fibrils means that this compound is weakly bound to Aβ. On the other hand, the weak binding would prevent bexarotene from prolonging the lag phase. Thus, our two main in vitro observations seem to contradict each other. In order to settle this problem at the atomic level, we have performed all-atom molecular dynamics simulations in explicit water. We have demonstrated that bexarotene is not capable to reduce amyloid deposits due to weak binding to Aβ fibrils. However, it delays the self-assembly through reduction of the β-content of Aβ monomers at high enough ligand concentrations. Bexarotene is the first compound which displays such an unusual behavior. We have also shown that bexarotene has a low binding propensity to Aβ monomer and dimer.
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Affiliation(s)
- Pham Dinh Quoc Huy
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward,
District 12, Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Division of Theoretical Physics, Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap, Vietnam
- Biomedical Engineering Department, University of Technology, VNU HCM
268 Ly Thuong Kiet Street, District 10, Ho
Chi Minh City, Vietnam
| | - Zuzana Bednarikova
- Department of Theoretical
Physics, University of Natural Sciences, VNU, 227 Nguyen Van Cu,
District 5, Ho Chi Minh City, Vietnam
| | - Le Huu Phuc
- Department of Biophysics Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040
01 Kosice, Slovakia
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology, VNU HCM
268 Ly Thuong Kiet Street, District 10, Ho
Chi Minh City, Vietnam
| | - Zuzana Gazova
- Department of Theoretical
Physics, University of Natural Sciences, VNU, 227 Nguyen Van Cu,
District 5, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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14
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Increased Processivity, Misincorporation, and Nucleotide Incorporation Efficiency in Sulfolobus solfataricus Dpo4 Thumb Domain Mutants. Appl Environ Microbiol 2017; 83:AEM.01013-17. [PMID: 28710267 DOI: 10.1128/aem.01013-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/04/2017] [Indexed: 01/21/2023] Open
Abstract
The present study aimed to increase the processivity of Sulfolobus solfataricus DNA polymerase Dpo4. Protein engineering and bioinformatics were used to compile a library of potential Dpo4 mutation sites. Ten potential mutants were identified and constructed. A primer extension assay was used to evaluate the processivity of Dpo4 mutants. Thumb (A181D) and finger (E63K) domain mutants showed a processivity of 20 and 19 nucleotides (nt), respectively. A little finger domain mutant (I248Y) exhibited a processivity of 17 nt, only 1 nt more than wild-type Dpo4. Furthermore, the A181D mutant showed lower fidelity and higher nucleotide incorporation efficiency (4.74 × 10-4 s-1 μM-1) than E63K and I248Y mutants. When tasked with bypassing damage, the A181D mutant exhibited a 3.81-fold and 2.62-fold higher catalytic efficiency (kcat/Km ) at incorporating dCTP and dATP, respectively, than wild-type Dpo4. It also showed a 55% and 91.5% higher catalytic efficiency when moving beyond the damaged 8-oxoG:C and 8-oxoG:A base pairs, respectively, compared to wild-type Dpo4. Protein engineering and bioinformatics methods can effectively increase the processivity and translesion synthesis ability of Dpo4.IMPORTANCE DNA polymerases with poor fidelity can be exploited to store data and record changes in response to the intracellular environment. Sulfolobus solfataricus Dpo4 is such an enzyme, although its use is hindered by its low processivity. In this work, we used a bioinformatics and protein engineering approach to generate Dpo4 mutants with improved processivity. We identified the Dpo4 thumb domain as the most relevant in controlling processivity.
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15
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Thai NQ, Nguyen HL, Linh HQ, Li MS. Protocol for fast screening of multi-target drug candidates: Application to Alzheimer's disease. J Mol Graph Model 2017; 77:121-129. [PMID: 28850894 DOI: 10.1016/j.jmgm.2017.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023]
Abstract
The treatment of many diseases may require drugs that are capable to attack multiple targets simultaneously. Obviously, the virtual screening of multi-target drug candidates is much more time consuming compared to the single-target case. This, in particular, concerns the last step of virtual screening where the binding free energy is computed by conventional molecular dynamics simulation. To overcome this difficulty we propose a simple protocol which is relied on the fast steered molecular dynamics simulation and on available experimental data on binding affinity of reference ligand to a given target. Namely, first we compute non-equilibrium works generated during pulling ligands from the binding site using the steered molecular dynamics method. Then as top leads we choose only those compounds that have the non-equilibrium work larger than that of a reference compound for which the binding free energy has been already known from experiment. Despite many efforts no cures for AD (Alzheimer's disease) have been found. One of possible reasons for this failure is that drug candidates were developed for a single target, while there are exist many possible pathways to AD. Applying our new protocol to five targets including amyloid beta fibril, peroxisome proliferator-activated receptor γ, retinoic X receptor α, β- and γ-secretases, we have found two potential drugs (CID 16040294 and CID 9998128) for AD from the large PubChem database. We have also shown that these two ligands can interfere with the activity of popular Acetylcholinesterase target through strong binding towards it.
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Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Dong Thap University,783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Viet Nam; Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Hoang Linh Nguyen
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Mai Suan Li
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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16
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DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase. Sci Rep 2017; 7:4756. [PMID: 28684739 PMCID: PMC5500549 DOI: 10.1038/s41598-017-02578-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
DNA polymerase (pol) processivity, i.e., the bases a polymerase extends before falling off the DNA, and activity are important for copying difficult DNA sequences, including simple repeats. Y-family pols would be appealing for copying difficult DNA and incorporating non-natural dNTPs, due to their low fidelity and loose active site, but are limited by poor processivity and activity. In this study, the binding between Dbh and DNA was investigated to better understand how to rationally design enhanced processivity in a Y-family pol. Guided by structural simulation, a fused pol Sdbh with non-specific dsDNA binding protein Sso7d in the N-terminus was designed. This modification increased in vitro processivity 4-fold as compared to the wild-type Dbh. Additionally, bioinformatics was used to identify amino acid mutations that would increase stabilization of Dbh bound to DNA. The variant SdbhM76I further improved the processivity of Dbh by 10 fold. The variant SdbhKSKIP241–245RVRKS showed higher activity than Dbh on the incorporation of dCTP (correct) and dATP (incorrect) opposite the G (normal) or 8-oxoG(damaged) template base. These results demonstrate the capability to rationally design increases in pol processivity and catalytic efficiency through computational DNA binding predictions and the addition of non-specific DNA binding domains.
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17
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Chang YJ, Linh NH, Shih YH, Yu HM, Li MS, Chen YR. Alzheimer's Amyloid-β Sequesters Caspase-3 in Vitro via Its C-Terminal Tail. ACS Chem Neurosci 2016; 7:1097-106. [PMID: 27227450 DOI: 10.1021/acschemneuro.6b00049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Amyloid-β (Aβ), the main constituent in senile plaques found in the brain of patients with Alzheimer's disease (AD), is considered as a causative factor in AD pathogenesis. The clinical examination of the brains of patients with AD has demonstrated that caspase-3 colocalizes with senile plaques. Cellular studies have shown that Aβ can induce neuronal apoptosis via caspase-3 activation. Here, we performed biochemical and in silico studies to investigate possible direct effect of Aβ on caspase-3 to understand the molecular mechanism of the interaction between Aβ and caspase-3. We found that Aβ conformers can specifically and directly sequester caspase-3 activity in which freshly prepared Aβ42 is the most potent. The inhibition is noncompetitive, and the C-terminal region of Aβ plays an important role in sequestration. The binding of Aβ to caspase-3 was examined by cross-linking and proteolysis and by docking and all-atom molecular dynamic simulations. Experimental and in silico results revealed that Aβ42 exhibits a higher binding affinity than Aβ40 and the hydrophobic C-terminal region plays a key role in the caspase-Aβ interaction. Overall, our study describes a novel mechanism demonstrating that Aβ sequesters caspase-3 activity via direct interaction and facilitates future therapeutic development in AD.
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Affiliation(s)
- Yu-Jen Chang
- Genomics
Research Center, Academia Sinica, Taiwan, 128, Academia Road, Sec. 2, Nankang
Dist., Taipei 115, Taiwan
| | - Nguyen Hoang Linh
- Institute for Computational Science and Technology, SBI Building,
Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Yao Hsiang Shih
- Genomics
Research Center, Academia Sinica, Taiwan, 128, Academia Road, Sec. 2, Nankang
Dist., Taipei 115, Taiwan
| | - Hui-Ming Yu
- Genomics
Research Center, Academia Sinica, Taiwan, 128, Academia Road, Sec. 2, Nankang
Dist., Taipei 115, Taiwan
| | - Mai Suan Li
- Institute of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Yun-Ru Chen
- Genomics
Research Center, Academia Sinica, Taiwan, 128, Academia Road, Sec. 2, Nankang
Dist., Taipei 115, Taiwan
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18
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Thai NQ, Tseng NH, Vu MT, Nguyen TT, Linh HQ, Hu CK, Chen YR, Li MS. Discovery of DNA dyes Hoechst 34580 and 33342 as good candidates for inhibiting amyloid beta formation: in silico and in vitro study. J Comput Aided Mol Des 2016; 30:639-50. [PMID: 27511370 PMCID: PMC5021751 DOI: 10.1007/s10822-016-9932-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/27/2016] [Indexed: 01/14/2023]
Abstract
Combining Lipinski's rule with the docking and steered molecular dynamics simulations and using the PubChem data base of about 1.4 million compounds, we have obtained DNA dyes Hoechst 34580 and Hoechst 33342 as top-leads for the Alzheimer's disease. The binding properties of these ligands to amyloid beta (Aβ) fibril were thoroughly studied by in silico and in vitro experiments. Hoechst 34580 and Hoechst 33342 prefer to locate near hydrophobic regions with binding affinity mainly governed by the van der Waals interaction. By the Thioflavin T assay, it was found that the inhibition constant IC50 ≈ 0.86 and 0.68 μM for Hoechst 34580 and Hoechst 33342, respectively. This result qualitatively agrees with the binding free energy estimated using the molecular mechanic-Poisson Boltzmann surface area method and all-atom simulations with the AMBER-f99SB-ILDN force field and water model TIP3P. In addition, DNA dyes have the high capability to cross the blood brain barrier. Thus, both in silico and in vitro experiments have shown that Hoechst 34580 and 33342 are good candidates for treating the Alzheimer's disease by inhibiting Aβ formation.
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Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Vietnam
- Division of Theoretical Physics, Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap Vietnam
| | - Ning-Hsuan Tseng
- Genomics Research Center, Academia Sinica, Academia Rd., Sec. 2, Nankang Dist., Taipei 115, Taiwan
| | - Mui Thi Vu
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Tin Trung Nguyen
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Vietnam
| | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, 128 Academia Road Section 2, Taipei, 11529 Taiwan
- National Center for Theoretical Sciences, National Tsing Hua University, 101 Kuang-Fu Road Section 2, Hsinch, 30013 Taiwan
- Business School, University of Shanghai for Science and Technology, 334 Jun Gong Road, Shanghai, 200093 China
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Academia Rd., Sec. 2, Nankang Dist., Taipei 115, Taiwan
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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19
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Ngo ST, Fang ST, Huang SH, Chou CL, Huy PDQ, Li MS, Chen YC. Anti-arrhythmic Medication Propafenone a Potential Drug for Alzheimer's Disease Inhibiting Aggregation of Aβ: In Silico and in Vitro Studies. J Chem Inf Model 2016; 56:1344-56. [PMID: 27304669 DOI: 10.1021/acs.jcim.6b00029] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia caused by the formation of Aβ aggregates. So far, no effective medicine for the treatment of AD is available. Many efforts have been made to find effective medicine to cope with AD. Curcumin is a drug candidate for AD, being a potent anti-amyloidogenic compound, but the results of clinical trials for it were either negative or inclusive. In the present study, we took advantages from accumulated knowledge about curcumin and have screened out four compounds that have chemical and structural similarity with curcumin more than 80% from all FDA-approved oral drugs. Using all-atom molecular dynamics simulation and the free energy perturbation method we showed that among predicted compounds anti-arrhythmic medication propafenone shows the best anti-amyloidogenic activity. The in vitro experiment further revealed that it can inhibit Aβ aggregation and protect cells against Aβ induced cytotoxicity to almost the same extent as curcumin. Our results suggest that propafenone may be a potent drug for the treatment of Alzheimer's disease.
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Affiliation(s)
- Son Tung Ngo
- Institute for Computational Science and Technology , Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Institute of Physics, Polish Academy of Sciences , Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | | | | | - Chao-Liang Chou
- Department of Neurology, Mackay Memorial Hospital , New Taipei City, 252 Taiwan
| | - Pham Dinh Quoc Huy
- Institute for Computational Science and Technology , Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Institute of Physics, Polish Academy of Sciences , Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences , Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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20
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Nguyen TT, Tran DP, Hoang Z, Carloni P, Van Pham P, Nguyen C, Li MS. Ligand binding to anti-cancer target CD44 investigated by molecular simulations. J Mol Model 2016; 22:165. [PMID: 27342250 DOI: 10.1007/s00894-016-3029-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
Abstract
CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 in a cell-based assay. In this study, we investigated the mechanism and energetics of F-19848A binding to CD44 using molecular simulation. Using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) method, we obtained the binding free energy and inhibition constant of the complex. The van der Waals (vdW) interaction and the extended portion of F-19848A play key roles in the binding affinity. We screened natural products from a traditional Chinese medicine database to search for CD44 inhibitors. From combining pharmaceutical requirements with docking and molecular dynamics simulations, we found ten compounds that are potentially better or equal to the F-19848A ligand at binding to CD44 receptor. Therefore, we have identified new candidates of CD44 inhibitors, based on molecular simulation, which may be effective small molecules for the therapy of breast cancer.
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Affiliation(s)
- Tin Trung Nguyen
- Institute for Computational Sciences and Technology, SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Duy Phuoc Tran
- University of Technology, Vietnam National University-Ho Chi Minh City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Zung Hoang
- Center for Molecular and NanoArchitecture (MANAR), Vietnam National University-Ho Chi Minh City, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Juelich, Juelich, Germany.
| | - Phuc Van Pham
- Stem Cell Research and Application Laboratory, University of Science, Vietnam National University, Ho Chi Minh City, Vietnam.
| | - Chuong Nguyen
- Theoretical Physics Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland.
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21
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Yang Z, Wu F, Yuan X, Zhang L, Zhang S. Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies. J Mol Graph Model 2016; 65:27-34. [PMID: 26905206 DOI: 10.1016/j.jmgm.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 01/09/2023]
Abstract
Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs.
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Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China; School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China.
| | - Fei Wu
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, PR China
| | - Lei Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China.
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22
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Nguyen H, Tran T, Fukunishi Y, Higo J, Nakamura H, Le L. Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method. J Chem Inf Model 2015; 55:1936-43. [DOI: 10.1021/acs.jcim.5b00319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hung Nguyen
- Life
Science Laboratory, Institute for Computational Science and Technology, Ho Chi
Minh City, Vietnam
| | - Tien Tran
- University of Technology, Ho Chi Minh City, Vietnam
| | - Yoshifumi Fukunishi
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Junichi Higo
- Institute
for Protein Research, Osaka University, Osaka, Japan
| | - Haruki Nakamura
- Institute
for Protein Research, Osaka University, Osaka, Japan
| | - Ly Le
- Life
Science Laboratory, Institute for Computational Science and Technology, Ho Chi
Minh City, Vietnam
- School
of Biotechnology, International University, Vietnam National University, Ho
Chi Minh City, Vietnam
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23
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Phanich J, Rungrotmongkol T, Sindhikara D, Phongphanphanee S, Yoshida N, Hirata F, Kungwan N, Hannongbua S. A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. Protein Sci 2015; 25:147-58. [PMID: 26044768 DOI: 10.1002/pro.2718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/09/2022]
Abstract
The binding affinity of oseltamivir to the influenza B neuraminidase and to its variants with three single substitutions, E119G, R152K, and D198N, is investigated by the MM/3D-RISM method. The binding affinity or the binding free energy of ligand to receptor was found to be determined by a subtle balance of two major contributions that largely cancel out each other: the ligand-receptor interactions and the dehydration free energy. The theoretical results of the binding affinity of the drug to the mutants reproduced the observed trend in the resistivity, measured by IC50 ; the high-level resistance of E119G and R152K, and the low-level resistance of D198N. For E119G and R152K, reduction of the direct drug-target interaction, especially at the mutated residue, is the main source of high-level oseltamivir resistance. This phenomenon, however, is not found in the D198N strain, which is located in the framework of the active-site.
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Affiliation(s)
- Jiraphorn Phanich
- Department of Chemistry, Computational Chemistry Unit Cell, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.,Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Daniel Sindhikara
- Schrödinger, Inc, 120 West 45th Street, 17th Floor, New York, New York, 10036
| | - Saree Phongphanphanee
- Department of Materials Science, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Sciences, Kyushu University, Fukuoka, 812-8581, Japan
| | - Fumio Hirata
- College of Life Sciences, Ritsumeikan University, and Molecular Design Frontier Co. Ltd, Kusatsu, 525-8577, Japan
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supot Hannongbua
- Department of Chemistry, Computational Chemistry Unit Cell, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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24
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Steered molecular dynamics approach for promising drugs for influenza A virus targeting M2 channel proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:447-55. [DOI: 10.1007/s00249-015-1047-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/20/2015] [Accepted: 05/14/2015] [Indexed: 01/14/2023]
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25
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Viet MH, Siposova K, Bednarikova Z, Antosova A, Nguyen TT, Gazova Z, Li MS. In Silico and in Vitro Study of Binding Affinity of Tripeptides to Amyloid β Fibrils: Implications for Alzheimer’s Disease. J Phys Chem B 2015; 119:5145-55. [DOI: 10.1021/acs.jpcb.5b00006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Man Hoang Viet
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Katarina Siposova
- Department
of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
- Department
of Biochemistry, Institute of Chemistry, Faculty of Science, P. J. Safarik University, Srobarova 2, 041
54 Kosice, Slovakia
| | - Zuzana Bednarikova
- Department
of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
- Department
of Biochemistry, Institute of Chemistry, Faculty of Science, P. J. Safarik University, Srobarova 2, 041
54 Kosice, Slovakia
| | - Andrea Antosova
- Department
of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
- Department
of Biochemistry, Institute of Chemistry, Faculty of Science, P. J. Safarik University, Srobarova 2, 041
54 Kosice, Slovakia
| | - Truc Trang Nguyen
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward,
District 12, Ho Chi Minh City, Vietnam
| | - Zuzana Gazova
- Department
of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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26
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Viet MH, Nguyen PH, Derreumaux P, Li MS. Effect of the English familial disease mutation (H6R) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci 2014; 5:646-57. [PMID: 24949887 DOI: 10.1021/cn500007j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The self-assembly of the amyloid beta (Aβ) peptides into senile plaques is the hallmark of Alzheimer's disease. Recent experiments have shown that the English familial disease mutation (H6R) speeds up the fibril formation process of alloforms Aβ40 and Aβ42 peptides altering their toxicity to cells. We used all-atom molecular dynamics simulations at microsecond time scales with the OPLS-AA force field and TIP4P explicit water model to study the structural dynamics of the monomer and dimer of H6R sequences of both peptides. The reason behind the self-assembly acceleration is common that upon mutation the net charge is reduced leading to the weaker repulsive interaction between chains that facilitates the peptide association. In addition, our estimation of the solvation free energy shows that the mutation enhances the hydrophobicity of both peptides speeding up their aggregation. However, we can show that the acceleration mechanisms are different for different peptides: the rate of fibril formation of Aβ42 increases due to increased β-structure at the C-terminal in both monomer and dimer and enhanced stability of salt bridge Asp23-Lys28 in monomer, while the enhancement of turn at residues 25-29 and reduction of coil in regions 10-13, 26-19, and 30-34 would play the key role for Aβ40. Overall, our study provides a detailed atomistic picture of the H6R-mediated conformational changes that are consistent with the experimental findings and highlights the important role of the N-terminal in Aβ peptide aggregation.
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Affiliation(s)
- Man Hoang Viet
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Denis Diderot, Paris Sorbonne Cité 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, Bvd Saint Michel, 75005 Paris, France
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward,
District 12, Ho Chi Minh City, Vietnam
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27
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Huy PDQ, Li MS. Binding of fullerenes to amyloid beta fibrils: size matters. Phys Chem Chem Phys 2014; 16:20030-40. [DOI: 10.1039/c4cp02348j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Effects of water models on binding affinity: evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase. ScientificWorldJournal 2014; 2014:536084. [PMID: 24672329 PMCID: PMC3929574 DOI: 10.1155/2014/536084] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/05/2013] [Indexed: 11/23/2022] Open
Abstract
The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔGbind of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔGbind is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is
no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields
ΔGbind decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM.
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29
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Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. J Comput Aided Mol Des 2013; 27:935-50. [DOI: 10.1007/s10822-013-9691-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/05/2013] [Indexed: 01/15/2023]
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30
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Pan P, Li L, Li Y, Li D, Hou T. Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. Antiviral Res 2013; 100:356-64. [DOI: 10.1016/j.antiviral.2013.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/07/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022]
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31
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Tran DTT, Le LT, Truong TN. Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase. J Comput Aided Mol Des 2013; 27:689-95. [PMID: 23979194 DOI: 10.1007/s10822-013-9675-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
Abstract
Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.
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Affiliation(s)
- Diem-Trang T Tran
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
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32
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Li L, Li Y, Zhang L, Hou T. Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. J Chem Inf Model 2012; 52:2715-29. [DOI: 10.1021/ci300375k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lin Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Liling Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
- College of
Pharmaceutical Sciences,
Soochow University, Suzhou, Jiangsu 215123, China
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33
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Ripoll DR, Khavrutskii IV, Chaudhury S, Liu J, Kuschner RA, Wallqvist A, Reifman J. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase. PLoS Comput Biol 2012; 8:e1002665. [PMID: 22956900 PMCID: PMC3431292 DOI: 10.1371/journal.pcbi.1002665] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 07/15/2012] [Indexed: 12/26/2022] Open
Abstract
Quantitatively predicting changes in drug sensitivity associated with residue mutations is a major challenge in structural biology. By expanding the limits of free energy calculations, we successfully identified mutations in influenza neuraminidase (NA) that confer drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD) with Hamiltonian Replica Exchange and calculated binding free energy changes for H274Y, N294S, and Y252H mutants. Based on experimental data, our calculations achieved high accuracy and precision compared with results from established computational methods. Analysis of 15 µs of aggregated MD trajectories provided insights into the molecular mechanisms underlying drug resistance that are at odds with current interpretations of the crystallographic data. Contrary to the notion that resistance is caused by mutant-induced changes in hydrophobicity of the binding pocket, our simulations showed that drug resistance mutations in NA led to subtle rearrangements in the protein structure and its dynamics that together alter the active-site electrostatic environment and modulate inhibitor binding. Importantly, different mutations confer resistance through different conformational changes, suggesting that a generalized mechanism for NA drug resistance is unlikely. The capacity of the influenza virus to rapidly mutate and render resistance to a handful of FDA approved neuraminidase (NA) inhibitors represents a significant human health concern. To gain an atomic-level understanding of the mechanisms behind drug resistance, we applied a novel computational approach to characterize resistant NA mutations. These results are comparable in accuracy and precision with the best experimental measurements presently available. To the best of our knowledge, this is the first time that a rigorous computational method has attained the level of certainty needed to predict subtle changes in binding free energies conferred by mutations. Analysis of our simulation data provided a thorough description of the thermodynamics of the binding process for different NA-inhibitor complexes, with findings that in some cases challenge current views based on interpretations of the crystallographic data. While we did not find a generalized mechanism of NA resistance, we identified key differences between oseltamivir and zanamivir that discriminate their responses to the three mutations we considered, namely H274Y, N294S and Y252H. It is worth noting that our approach can be broadly applied to predict resistant mutations to existing and newly developed drugs in other important drug targets.
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Affiliation(s)
- Daniel R. Ripoll
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, United States of America
| | - Ilja V. Khavrutskii
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, United States of America
| | - Sidhartha Chaudhury
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, United States of America
| | - Jin Liu
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, United States of America
| | - Robert A. Kuschner
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Research Unit, Silver Spring, Maryland, United States of America
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, United States of America
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, United States of America
- * E-mail:
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Ngo ST, Li MS. Curcumin binds to Aβ1-40 peptides and fibrils stronger than ibuprofen and naproxen. J Phys Chem B 2012; 116:10165-75. [PMID: 22877239 DOI: 10.1021/jp302506a] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Binding of curcumin, naproxen, and ibuprofen to Aβ1-40 peptide and its fibrils is studied by docking method and all-atom molecular dynamics simulations. The Gromos96 43a1 force field and simple point charge model of water have been used for molecular dynamics simulations. It is shown that if the receptor is a monomer then naproxen and ibuprofen are bound to the same place that is different from the binding position of curcumin. However all of three ligands have the same binding pocket in fibrillar structures. The binding mechanism is studied in detail showing that the van der Waals interaction between ligand and receptor dominates over the electrostatic interaction. The binding free energies obtained by the molecular mechanic-Poisson-Boltzmann surface area method indicate that curcumin displays higher binding affinity than nonsteroidal anti-inflammatory drugs. Our results are in good agreement with the experiments.
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Affiliation(s)
- Son Tung Ngo
- Institute for Computational Science and Technology , 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam, and
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35
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Kar P, Knecht V. Mutation-induced loop opening and energetics for binding of tamiflu to influenza N8 neuraminidase. J Phys Chem B 2012; 116:6137-49. [PMID: 22553951 DOI: 10.1021/jp3022612] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tamiflu, also known as oseltamivir (OTV), binds to influenza A neuraminidase (H5N1) with very high affinity (0.32 nM). However, this inhibitor binds to other neuraminidases as well. In the present work, a systematic computational study is performed to investigate the mechanism underlying the binding of oseltamivir to N8 neuraminidase (NA) in "open" and "closed" conformations of the 150-loop through molecular dynamics simulations and the popular and well established molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculation method. Whereas the closed conformation is stable for wild type N8, it transforms into the open conformation for the mutants Y252H, H274Y, and R292K, indicating that bound to oseltamivir these mutants are preferentially in the open conformation. Our calculations show that the binding of wild type oseltamivir to the closed conformation of N8 neuraminidase is energetically favored compared to the binding to the open conformation. We observe water mediated binding of oseltamivir to the N8 neuraminidase in both conformations which is not seen in the case of binding of the same drug to the H5N1 neuraminidase. The decomposition of the binding free energy reveals the mechanisms underlying the binding and changes in affinity due to mutations. Considering the mutant N8 variants in the open conformation adopted during the simulations, we observe a significant loss in the size of the total binding free energy for the N8(Y252H)-OTV, N8(H274Y)-OTV, and N8(R292K)-OTV complexes compared to N8(WT)-OTV, mainly due to the decrease in the size of the intermolecular electrostatic energy. For R292K, an unfavorable shift in the van der Waals interactions also contributes to the drug resistance. The mutations cause a significant expansion in the active site cavity, increasing its solvent accessible surface compared to the crystal structures of both the open and closed conformations. Our study underscores the need to consider dynamics in rationalizing the structure-function relationships of various antiviral inhibitor-NA complexes.
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Affiliation(s)
- Parimal Kar
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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36
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Hercend C, Bauvais C, Bollot G, Delacotte N, Chappuis P, Woimant F, Launay JM, Manivet P. Elucidation of the ATP7B N-domain Mg2+-ATP coordination site and its allosteric regulation. PLoS One 2011; 6:e26245. [PMID: 22046264 PMCID: PMC3203118 DOI: 10.1371/journal.pone.0026245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Accepted: 09/23/2011] [Indexed: 11/25/2022] Open
Abstract
The diagnostic of orphan genetic disease is often a puzzling task as less attention is paid to the elucidation of the pathophysiology of these rare disorders at the molecular level. We present here a multidisciplinary approach using molecular modeling tools and surface plasmonic resonance to study the function of the ATP7B protein, which is impaired in the Wilson disease. Experimentally validated in silico models allow the elucidation in the Nucleotide binding domain (N-domain) of the Mg2+-ATP coordination site and answer to the controversial role of the Mg2+ ion in the nucleotide binding process. The analysis of protein motions revealed a substantial effect on a long flexible loop branched to the N-domain protein core. We demonstrated the capacity of the loop to disrupt the interaction between Mg2+-ATP complex and the N-domain and propose a role for this loop in the allosteric regulation of the nucleotide binding process.
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Affiliation(s)
- Claude Hercend
- APHP, Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France
- INSERM U942, Biomarqueurs et Insuffisance cardiaque, Hôpital Lariboisière, Paris, France
| | - Cyril Bauvais
- Division of Structural Biology, Bioquanta, Paris, France
| | | | | | - Philippe Chappuis
- APHP, Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France
| | - France Woimant
- APHP, Hôpital Lariboisière, Service de Neurologie, Paris, France
| | - Jean-Marie Launay
- APHP, Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France
- INSERM U942, Biomarqueurs et Insuffisance cardiaque, Hôpital Lariboisière, Paris, France
| | - Philippe Manivet
- APHP, Hôpital Lariboisière, Service de Biochimie et de Biologie Moléculaire, Paris, France
- INSERM U829, SABNP Laboratory, Evry, France
- Université Evry Val-d'Essonne, Evry, France
- * E-mail:
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