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Shirani H, Hashemianzadeh SM. Quantum-level machine learning calculations of Levodopa. Comput Biol Chem 2024; 112:108146. [PMID: 39067350 DOI: 10.1016/j.compbiolchem.2024.108146] [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: 02/14/2024] [Revised: 06/20/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
Many drug molecules contain functional groups, resulting in a torsional barrier corresponding to rotation around the bond linking the fragments. In medicinal chemistry and pharmaceutical sciences, inclusive of drug design studies, the exact calculation of the potential energy surface (PES) of these molecular torsions is extremely important and precious. Machine learning (ML), including deep learning (DL), is currently one of the most rapidly evolving tools in computer-aided drug discovery and molecular simulations. In this work, we used ANI-1x neural network potential as a quantum-level ML to predict the PESs of the L-3,4-dihydroxyphenylalanine (Levodopa) antiparkinsonian drug molecule. The electronic energies and structural parameters calculated by density functional theory (DFT) using the wB97X method and all possible Pople's basis sets indicated the 6-31G(d) basis set, when used with the wB97X functional, exhibits behavior similar to that of the ANI-1x model. The vibrational frequencies investigation showed a linear correlation between DFT and ML data. All ANI-1x calculations were completed quickly in a very short computing time. From this perspective, we expect the ANI-1x dataset applied in this work to be appreciably efficient and effective in computational structure-based drug design studies.
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Affiliation(s)
- Hossein Shirani
- Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science and Technology, P.O. Box 16846-13114, Tehran, Iran.
| | - Seyed Majid Hashemianzadeh
- Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science and Technology, P.O. Box 16846-13114, Tehran, Iran.
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Intramolecular interactions (O-H∙∙∙O, C-H∙∙∙N, N-H∙∙∙π) in isomers of neutral, cation, and anion dopamine molecules: A DFT study on the influence of solvents (water and ethanol). J Mol Model 2023; 29:67. [PMID: 36773132 DOI: 10.1007/s00894-023-05466-y] [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: 12/21/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023]
Abstract
CONTEXT Dopamine (DA) is one of the most important neurotransmitters associated with numerous neural disorders. This investigation reports the intramolecular interactions present in the isomers of neutral (DA0), anionic (DA-), and cationic (DA+) dopamine isomers in gas, water, and ethanol mediums. Neutral and anion isomers have O-H∙∙∙O, C-H∙∙∙N intramolecular hydrogen bonds and N-H∙∙∙π interactions. All the interactions are electrostatic in nature. Isomers of cation dopamine show no intramolecular interactions in the solvent. Natural charges from natural bond orbital (NBO) analysis show that O-H∙∙∙O bonds and the N-H∙∙∙π interactions are the most and least polar, respectively. 1H NMR study reveals the inverse linear correlation between shielding constant and electron density in a solvent medium. HOMO-LUMO energy gap indicates higher stability for neutral and cationic forms of dopamine isomers in water and ethanol medium. METHODS We have optimized all the structural forms of dopamine molecule using the Becke three hybrid exchange and Lee-Yang-Parr correlation functional with Grimme's dispersion correction, B3LYP-D3(BJ), and aug-cc-pVTZ basis set using the Gaussian16 software. Vibrational frequency analysis with no imaginary frequencies confirms the nature of global minima. The solvent studies (water and ethanol) were carried out using the SCRF keyword and the polarisable continuum model (PCM) of Miertus and Tomasi. NBO analysis and NMR studies were also performed for all conformers. Topology analysis was explored using the software Multiwfn.
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Unveiling the nature of interactions in the supramolecular complex of Cucurbit [7-8] uril with ascorbic acid, dopamine and uric acid for biosensing applications: a computational study. Struct Chem 2022. [DOI: 10.1007/s11224-022-01945-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Janani S, Rajagopal H, Muthu S, Aayisha S, Raja M, Irfan A. Structural, vibrational, electronic properties, hirshfeld surface analysis topological and molecular docking studies of N-[2-(diethylamino)ethyl]-2-methoxy-5-methylsulfonylbenzamide. Heliyon 2021; 7:e08186. [PMID: 34712858 PMCID: PMC8531569 DOI: 10.1016/j.heliyon.2021.e08186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/25/2021] [Accepted: 10/13/2021] [Indexed: 12/01/2022] Open
Abstract
The theoretical (Freebase, Cationic species) and experimental investigations on the molecular structural, spectroscopic characterization, and electronic properties of N2M5MB are reported. The most stable structure of the N2M5MB was analysed by employing Density Functional Theory (DFT) at different functional such as B3LYP, PBEPBE, TPSSTPSS and IEF-PCM (Freebase) and Cationic (B3LYP, IEF-PCM)/ 6-311++G (d,p) basis set level. The Potential Energy Scan (PES) analysis has been employed to investigate the conformational preference of the title molecule. The optimized molecular geometry, vibrational assignments (FT-IR, FT-Raman) of wavenumbers have been performed for freebase, cationic species (Gas, PCM) for the individual modes of vibration. The experimental UV-Vis absorption spectrum was obtained and compared with the simulated (Freebase, Cationic species) Time-Dependent (TD-DFT-M062X) method. The FMO's, electron-hole distributions, HOMA, FLU, Hirshfeld surface analysis, Electrostatic potential surface (ESP), Fukui functions, and topological parameters were discussed. Molecular docking studies were performed for the N2M5MB (ligand) into the active site of targeted proteins (1H22, 4DTL, 5OV9) which belong to AChE inhibitors with the minimum binding energy was detected.
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Affiliation(s)
- S. Janani
- Department of Physics, Queen Mary's College, Chennai, 600004, Tamilnadu, India
- University of Madras, Chennai, 600005, Tamilnadu, India
| | - Hemamalini Rajagopal
- Department of Physics, Queen Mary's College, Chennai, 600004, Tamilnadu, India
- University of Madras, Chennai, 600005, Tamilnadu, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604407, Tamilnadu, India
- Department of Physics, Puratchi Thalaivar Dr.M.G.R Govt. Arts and Science College, Uthiramerur 603406, Tamilnadu, India
| | - S. Aayisha
- Department of Physics, Meenakshi College for Women, Chennai, 600024, Tamilnadu, India
| | - M. Raja
- Department of Physics, Govt. Thirumagal Mills College, Gudiyattam, Vellore 632602, India
| | - Ahmad Irfan
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
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