1
|
Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure. JOURNAL OF CHEMICAL RESEARCH 2022. [DOI: 10.1177/17475198221101999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.
Collapse
|
2
|
Wang C, Jiang Y, Zhang R, Lin Z. Intermolecular π/π and H/π interactions in dimers researched by different computational methods. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The analysis of π/π and H /π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H /π interactions by calculating the binding energies of five benzene-containing dimers. The effects of 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results were analyzed too. We found that the DFTB-D and B97D methods combined with the 6-311++G** basis set perform well for dimers that contain π/π and H /π interactions. With high efficiency and satisfactory precision, DFTB-D is helpful for the calculation of complexes containing π/π and H /π stacking. We further calculated the structures and properties of phenylalanine-containing dimers using the DFTB-D and B97D methods. The properties of low energy conformers such as rotational constants, dipole moments and molecular orbitals were also analyzed. These data should be helpful for research into systems that contain π/π and H /π stacking.
Collapse
Affiliation(s)
- Cuihong Wang
- School of Science, TianJin ChengJian University, Tianjin 300384, P. R. China
| | - Yue Jiang
- School of Science, TianJin ChengJian University, Tianjin 300384, P. R. China
| | - Ruiqin Zhang
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, P. R. China
| | - Zijing Lin
- Department of Physics & Collaborative Innovation Center of Suzhou Nano Science and Technology, University of Science and Technology of China, Hefei 230026, P. R. China
| |
Collapse
|
3
|
Li J, Hou Z, Chen GH, Li F, Zhou Y, Xue XY, Li ZP, Jia M, Zhang ZD, Li MK, Luo XX. Synthesis, antibacterial activities, and theoretical studies of dicoumarols. Org Biomol Chem 2014; 12:5528-35. [DOI: 10.1039/c4ob00772g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, we report the synthesis, evaluation of antibacterial activity and theoretical study of dicoumarols including DC, 2-PyDC, 3-PyDC and 4-PyDC.
Collapse
Affiliation(s)
- Jing Li
- School of Chemistry and Chemical Engineering
- Xi'an University of Arts and Sciences
- Xi'an, China
| | - Zheng Hou
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Guang-Hui Chen
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Fen Li
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Ying Zhou
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Xiao-Yan Xue
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Zhou-Peng Li
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Min Jia
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Zi-Dan Zhang
- Department of Physics
- School of Science
- Tianjin University
- Tianjin, China
| | - Ming-Kai Li
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| | - Xiao-Xing Luo
- Department of Pharmacology
- School of Pharmacy
- the Fourth Military Medical University
- Xi'an, China
| |
Collapse
|
4
|
FU TING, WU XUE, XIU ZHILONG, WANG JINGUANG, YIN LIU, LI GUOHUI. UNDERSTANDING THE MOLECULAR MECHANISM OF BINDING MODES OF AURORA A INHIBITORS BY LONG TIME SCALE GPU DYNAMICS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Inhibition of Aurora A kinase interaction is considered to be a promising approach for the discovery of new molecularly targeted cancer therapeutics. In this study, the binding mechanisms of two different inhibitors with a contrasting binding affinity to Aurora A were investigated by long time scale GPU molecular dynamics (MD) simulations coupled with molecular mechanics-Poisson–Boltzmann/generalized Born surface area (MM-PB/GBSA) method. The results showed that the predicted binding free energies of these two complexes were consistent with the experimental data. Through analyzing the individual energy components of binding free energy, we found that the van der Waals contribution was the main force to drive the inhibitor–protein binding and the electrostatic contribution was also a crucial factor for the inhibitor–Aurora A binding. The structural analysis demonstrated that the inhibitor HPM could produce more hydrophobic interaction contacts with Aurora A than that of 2JZ, and the loss of key hydrogen bonds between the inhibitor and residue Arg137 in the hinge region of Aurora A was another important reason for the weaker binding affinity of 2JZ to Aurora A. This study sheds more light on the development of the efficient inhibitors targeting the Aurora A.
Collapse
Affiliation(s)
- TING FU
- Department of Bioscience and Biotechnology, School of Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd., Dalian 116023, P. R. China
- Graduate University of the Chinese Academy of Sciences 19A Yuquanlu, Beijing 100049, P. R. China
| | - XUE WU
- Department of Bioscience and Biotechnology, School of Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd., Dalian 116023, P. R. China
- Graduate University of the Chinese Academy of Sciences 19A Yuquanlu, Beijing 100049, P. R. China
| | - ZHILONG XIU
- Department of Bioscience and Biotechnology, School of Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, P. R. China
| | - JINGUANG WANG
- Thoracic Surgery Department in the 1st Affiliated, Hospital of Dalian Medical University, 222 Zhongshan Road Dalian, Liaoning Province, China 116011, P. R. China
| | - LIU YIN
- Oncology Department in the 1st Affiliated, Hospital of Dalian Medical University, 222 Zhongshan Road, Dalian, Liaoning Province, China 116011, P. R. China
| | - GUOHUI LI
- Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd., Dalian 116023, P. R. China
| |
Collapse
|
5
|
MENG FANCUI. MOLECULAR SIMULATION OF α-TOCOPHEROL PASSING ACROSS DPPC LIPID USING POTENTIAL OF MEAN FORCE AND ACCELERATED MOLECULAR DYNAMICS METHOD. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper the process of α-tocopherol (TCP) passing across DPPC membrane was simulated using both the potential of mean force (PMF) and the accelerated molecular dynamics (aMD) methods, respectively. Energy properties, hydrogen bonds and orientation have been compared between these two methods and several conclusions have been obtained. The results indicate that TCP tends to stay at z = 1.2 nm of lipid bilayer. The binding free energy profiles of these two methods are alike. All these show that aMD could obtain comparable results as PMF method, while needs less computation time and resources. Therefore, aMD method could be used as an alternative method for prediction of transport properties of drug-lipid system.
Collapse
Affiliation(s)
- FANCUI MENG
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, P. R. China
- State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, P. R. China
| |
Collapse
|
6
|
KABANDA MWADHAMM, EBENSO ENOE. DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.
Collapse
Affiliation(s)
- MWADHAM M. KABANDA
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
| | - ENO E. EBENSO
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
| |
Collapse
|
7
|
LUO QIQUAN, BELLER MATTHIAS, JIAO HAIJUN. FORMIC ACID DEHYDROGENATION ON SURFACES — A REVIEW OF COMPUTATIONAL ASPECT. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613300012] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this review, we have mainly shown the recent computational studies on formic acid adsorption and selective dissociation to produce hydrogen ( HCOOH → CO 2 + H 2) on several metal ( Pt , Pd , Ni , Cu , Rh and Au ) and metal oxide ( TiO 2, MgO , ZnO and NiO ) surfaces, and both thermal decomposition and electro-catalytic oxidation have been discussed. The decomposition mechanisms of formic acid have been studied by using different computational models and methods, not only interesting and exciting but also different and controversial results have been reported. It is noted that the model systems used in these studies are too simple and idealized, and they cannot represent the real catalysts or the catalytic systems, and more sophisticated computational methodologies and real model systems under the consideration of the working conditions are therefore needed.
Collapse
Affiliation(s)
- QIQUAN LUO
- Leibniz-Institut für Katalyse e.V. an der Universität Rostock, Albert-Einstein-Strasse 29a, 18059 Rostock, Germany
| | - MATTHIAS BELLER
- Leibniz-Institut für Katalyse e.V. an der Universität Rostock, Albert-Einstein-Strasse 29a, 18059 Rostock, Germany
| | - HAIJUN JIAO
- Leibniz-Institut für Katalyse e.V. an der Universität Rostock, Albert-Einstein-Strasse 29a, 18059 Rostock, Germany
| |
Collapse
|