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Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Luo Q, Li G, Xiao J, Yin C, He Y, Wang M, Ma C, Zhu C, Xu J. DFT study on the hydrolysis of metsulfuron-methyl: A sulfonylurea herbicide. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sulfonylureas are an important group of herbicides widely used for a range of weeds and grasses control particularly in cereals. However, some of them tend to persist for years in environments. Hydrolysis is the primary pathway for their degradation. To understand the hydrolysis behavior of sulfonylurea herbicides, the hydrolysis mechanism of metsulfuron-methyl, a typical sulfonylurea, was investigated using density functional theory (DFT) at the B3LYP/6-31[Formula: see text]G(d,p) level. The hydrolysis of metsulfuron-methyl resembles nucleophilic substitution by a water molecule attacking the carbonyl group from aryl side (pathway a) or from heterocycle side (pathway b). In the direct hydrolysis, the carbonyl group is directly attacked by one water molecule to form benzene sulfonamide or heterocyclic amine; the free energy barrier is about 52–58[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. In the autocatalytic hydrolysis, with the second water molecule acting as a catalyst, the free energy barrier, which is about 43–45[Formula: see text]kcal[Formula: see text]mol[Formula: see text], is remarkably reduced by about 11[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is obvious that water molecules play a significant catalytic role during the hydrolysis of sulfonylureas.
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Affiliation(s)
- Qiuhan Luo
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Gang Li
- Weifang University of Science and Technology, Shouguang, Shangdong 262700, P. R. China
| | - Junping Xiao
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Chunhui Yin
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Yahui He
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Mingliang Wang
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Chensheng Ma
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Caizhen Zhu
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Jian Xu
- Institute of Low-Dimensional Materials Genome Initiative, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
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Balamurugan K, Murugan NA, Ågren H. Multistep Modeling Strategy To Improve the Binding Affinity Prediction of PET Tracers to Aβ 42: Case Study with Styrylbenzoxazole Derivatives. ACS Chem Neurosci 2016; 7:1698-1705. [PMID: 27626391 DOI: 10.1021/acschemneuro.6b00216] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Positron emission tomography (PET) tracers play an important role in the diagnosis of Alzheimer's disease, a condition that leads to progressive dementia and memory loss. A high binding affinity and specificity of the PET tracers to amyloid oligomers and fibrils are crucial for their successful application as diagnostic agents. In this sense, it is essential to design PET tracers with enhanced binding affinities, which can lead to more precise and earlier detection of Alzheimer's disease conditions. The application of in silico methodology for the design and development of efficient PET tracers may serve as an important route to improved Alzheimer's disease diagnosis. In this work, the performance of widely used computational methods is explored for predicting experimental binding affinities of styrylbenzoxazole (SB) derivatives against a common amyloid protofibril. By performing docking, molecular dynamics, and quantum chemistry calculations in sequence their combined predictive performance is explored. The present work emphasizes the merits as well as limitations of these simulation strategies in the realm of designing PET tracers for Alzheimer's disease diagnosis.
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Affiliation(s)
- Kanagasabai Balamurugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Natarajan Arul Murugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
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4
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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5
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Cao J, Liu Y, Shi A, Yuan Y, Wang M. A DFT study on the mechanism of reaction between 2, 4-diisocyanatotolune and cellulose. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The reaction mechanisms between 2, 4-Diisocyanatotolune (2, 4-TDI) and cellulose have been investigated using the density functional theory at the B3LYP/6-31[Formula: see text]G (d, p) level. The calculations show that the direct addition of 2, 4-TDI and cellulose possesses an unrealistically high barrier of 32–34[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. With a neighboring [Formula: see text]-d-glucose serving as a proton transporter by forming a flexible six-membered ring transition state, the energy barrier of the reaction is significantly reduced to 16–18 kcal[Formula: see text]mol[Formula: see text], which is in a good accordance with the experimental activation energy of 13.9–16.7[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is indicated that the reaction between 2, 4-TDI and cellulose is auto-catalyzed with a neighboring [Formula: see text]-d-glucose acting as a reactive catalyst.
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Affiliation(s)
- Jiping Cao
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, P. R. China
| | - Yali Liu
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
| | - Aijuan Shi
- Xi’an Modern Chemistry Research Institute, Xi’an 710065, P. R. China
| | - Yuan Yuan
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
| | - Mingliang Wang
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
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Yuan Y, Cao J, Liu Y, Shi A, Zhang Q, Lin X, Wang M. Catalytic Effects of Water Clusters on the Hydrolysis of Toluene-2,4-diisocyanate: A DFT Study. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yuan Yuan
- College of Chemistry and Chemical Engineering, Shenzhen University
| | - Jiping Cao
- Xi’an Modern Chemistry Research Institute
| | - Yali Liu
- College of Chemistry and Chemical Engineering, Shenzhen University
| | - Aijuan Shi
- Xi’an Modern Chemistry Research Institute
| | - Qing Zhang
- College of Chemistry and Chemical Engineering, Shenzhen University
| | - Xiaoxiong Lin
- College of Chemistry and Chemical Engineering, Shenzhen University
| | - Mingliang Wang
- College of Chemistry and Chemical Engineering, Shenzhen University
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Yuan Y, Hu W, Chi X, Li C, Gui D, Wang M, Liu J, Ma X, Pang A. First principle simulation on oxidation mechanism of diethyl ether by nitrogen dioxide. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615500200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The oxidation mechanism of diethyl ethers by NO2was carried out using density functional theory (DFT) at the B3LYP/6-31+G (d, p) level. The oxidation process of ether follows four steps. First, the diethyl ether reacts with NO2to produce HNO2and diethyl ether radical with an energy barrier of 20.62 kcal ⋅ mol-1. Then, the diethyl ether radical formed in the first step directly combines with NO2to form CH3CH ( ONO ) OCH2CH3. In the third step, the CH3CH ( ONO ) OCH2CH3was further decomposed into the CH3CH2ONO and CH3CHO with a moderately high energy barrier of 32.87 kcal ⋅ mol-1. Finally, the CH3CH2ONO continues to react with NO2to yield CH3CHO , HNO2and NO with an energy barrier of 28.13 kcal ⋅ mol-1. The calculated oxidation mechanism agrees well with Nishiguchi and Okamoto's experiment and proposal.
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Affiliation(s)
- Yuan Yuan
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
| | - Wei Hu
- Hubei Institute of Aerospace Chemotechnology, Xiangfan, Hubei 441003, P. R. China
| | - Xuhui Chi
- Hubei Institute of Aerospace Chemotechnology, Xiangfan, Hubei 441003, P. R. China
| | - Cuihua Li
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
| | - Dayong Gui
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
| | - Mingliang Wang
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
| | - Jianhong Liu
- College of Chemistry and Chemical Engineering, Shenzhen University, Guangdong 518060, P. R. China
| | - Xingang Ma
- Hubei Institute of Aerospace Chemotechnology, Xiangfan, Hubei 441003, P. R. China
| | - Aimin Pang
- Hubei Institute of Aerospace Chemotechnology, Xiangfan, Hubei 441003, P. R. China
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Ciancetta A, Genheden S, Ryde U. A QM/MM study of the binding of RAPTA ligands to cathepsin B. J Comput Aided Mol Des 2011; 25:729-42. [PMID: 21701919 DOI: 10.1007/s10822-011-9448-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/13/2011] [Indexed: 11/28/2022]
Abstract
We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson-Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r (2)) of 0.35-0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r (2) = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r (2) = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r (2) = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.
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Affiliation(s)
- Antonella Ciancetta
- Dipartimento di Scienze del Farmaco, Università degli Studi "G. D'Annunzio" Chieti-Pescara, Italy
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