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Bendaas R, Bekkar Y, Messaadia L, Bourougaa L, Messaoudi A, Kiamouche S, Messaoud B. Computational-based investigation of antioxidative potential polyphenolic compounds of Salvia officinalis L.: combined DFT and molecular docking approaches. J Mol Model 2024; 30:87. [PMID: 38416254 DOI: 10.1007/s00894-024-05866-8] [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: 12/12/2023] [Accepted: 02/03/2024] [Indexed: 02/29/2024]
Abstract
CONTEXT The antioxidant properties of the three polyphenolic compounds (carnosol, cirsiliol, and luteolin) of Salvia officinalis L. were investigated employing the density functional theory (DFT) calculations at the B3LYP of basis set at 6-311 + + G (d, p) in order to evaluate their antioxidant activity. The enthalpies of reactions associated with the SET-PT, SPLET, and HAT mechanisms were analyzed in gas and in different solvents using the CPCM (conductor-like polarizable continuum) model. For all possible hydrogen donor sites, the corresponding parameters (BDE, AIP, PDE, PA, ETE, HOMOs, and LUMOs) and reactivity indices (IPE, EA, Χ, η, S, and ω) were also evaluated. The calculated results showed that derivatives 12-OH, 11-OH, 4'-OH, and 3'-OH had the lowest antioxidant activity. The results showed as well that carnosol, cirsiliol, and luteolin have higher reactivity compared to ascorbic acid and could be considered better antioxidants. According to research, the catechol group is crucial in influencing the studied compounds antioxidant activity. The theoretically predicted order of antioxidant efficiencies in this work agrees well with the QSAR (quantitative structure-activity relationship) data. The findings show that in the vacuum as well as benzene media. HAT would be the most effective mechanism; in contrast, the thermodynamic equilibrium approach in polar media is the SPLET mechanism. Likewise, the outcomes of the docking modeling confirm that the selected molecules have high inhibitory activity to glutathione-S-transferases (GSTs) receptors. Moreover, they have very important pharmacokinetic, chemical, and biological profiles. Finally, all the results show that the three natural molecules have good pharmacokinetic profiles, particularly the bioavailability and permeability toward biological membranes. METHODS The software packages used in this investigation are Gaussian 16, Discovery studio Visualizer, and AutoDock vina. The three compounds (carnosol, cirsiliol, and luteolin) of Salvia officinalis L. were optimized with DFT/B3LYP of basis set at 6-311 + + G (d, p). The optimized structures were established via vibrational analysis (i.e., no imaginary frequencies in the frequency set). All enthalpies were zero-point (ZPE) corrected. Vibrational frequency calculations were performed at 298.15 K and 1 atmosphere pressure to determine the thermodynamic characteristics of the investigated reactions. The descriptors were associated with the antioxidant mechanisms for investigated molecules in vacuum and in various solvents. The molecular docking was used by AutoDock vina to estimate and evaluate the title compounds compatibility as potential antioxidant drugs utilizing appropriate receptor proteins. The solvation effect in the medium of benzene (ɛ = 2.27) and water (ɛ = 78.39) was taken into account. Furthermore, a methanol solvent (ɛ = 32.61) was also taken into consideration to compare with the empirical data.
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Affiliation(s)
- Ridha Bendaas
- Laboratory of Applied Energy and Materials (LEAM), University of Jijel, Jijel, Algeria
| | - Yahia Bekkar
- Laboratory of Valorization and Technology of Sahara Resources (VTRS), University of El Oued, B.P.789, 39000, El Oued, Algeria
| | - Lyamine Messaadia
- Laboratory of Applied Energy and Materials (LEAM), University of Jijel, Jijel, Algeria.
| | - Lotfi Bourougaa
- Laboratory of Molecular Chemistry and Environment (LMCE), University of Biskra, BP 145, 707000, Biskra, Algeria
| | - Abdelatif Messaoudi
- Laboratoire de Chimie Des Matériaux Et Des Vivants: Activité & Réactivité (LCMVAR), Département Chimie, Faculté Des Sciences de La Matière, Université de Batna 1, Batna, Algeria
| | - Samir Kiamouche
- Laboratory of Applied Energy and Materials (LEAM), University of Jijel, Jijel, Algeria
- Department of Environmental Engineering, Faculty of Engineering Process, University Constantine 3, 25000, Constantine, Algeria
| | - Benamira Messaoud
- Laboratory of Materials Interaction and Environment (LIME), Faculty of Exact Sciences and Computer Science, University of Jijel, 18000, Jijel, Algeria
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Bui TQ, Dat TTH, Quy PT, Hai NTT, Thai NM, Phu NV, Tuan LV, Huynh LK, Li MS, Nhung NTA. Identification of potential anti-hyperglycemic compounds in Cordyceps militaris ethyl acetate extract: in vitro and in silico studies. J Biomol Struct Dyn 2023:1-17. [PMID: 37997953 DOI: 10.1080/07391102.2023.2283156] [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: 05/15/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Cordyceps militaris has been long known for valuable health benefits by folk experience and was recently reported with diabetes-tackling evidences, thus deserving extending efforts on screening for component-activity relationship. In this study, experiments were carried out to find the evidence, justification, and input for computations on the potential against diabetes-related protein structures: PDB-4W93, PDB-3W37, and PDB-4A3A. Liquid chromatography identified 14 bioactive compounds in the ethyl acetate extract (1-14) and quantified the contents of cordycepin (0.11%) and adenosine (0.01%). Bioassays revealed the overall potential of the extract against α-amylase (IC50 = 6.443 ± 0.364 mg.mL-1) and α-glucosidase (IC50 = 2.580 ± 0.194 mg.mL-1). A combination of different computational platforms was used to select the most promising candidates for applications as anti-diabetic bio-inhibitors, i.e. 1 (ground state: -888.49715 a.u.; dipole moment 3.779 Debye; DS ¯ -12.3 kcal.mol-1; polarizability 34.7 Å3; logP - 1.30), 10 (ground state: -688.52406 a.u.; dipole moment 5.487 Debye; DS ¯ -12.6 kcal.mol-1; polarizability 24.9 Å3; logP - 3.39), and 12 (ground state: -1460.07276 a.u.; dipole moment 3.976 Debye; DS ¯ -12.5 kcal.mol-1; polarizability 52.4 Å3; logP - 4.39). The results encourage further experimental tests on cordycepin (1), mannitol (10), and adenosylribose (12) to validate their in-practice diabetes-related activities, thus conducive to hypoglycemic applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thanh Q Bui
- Department of Chemistry, University of Sciences, Hue University, Hue, Vietnam
| | - Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), Hue, Vietnam
| | - Phan Tu Quy
- Department of Natural Sciences & Technology, Tay Nguyen University, Dak Lak, Vietnam
| | | | - Nguyen Minh Thai
- Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Nguyen Vinh Phu
- Faculty of Basic Sciences, University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Le Van Tuan
- Department of Environmental Science, University of Sciences, Hue University, Hue City, Vietnam
| | - Lam K Huynh
- School of Chemical and Environmental Engineering, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Ho Chi Minh City, Vietnam
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Nguyen Thi Ai Nhung
- Department of Chemistry, University of Sciences, Hue University, Hue, Vietnam
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Basha AA, Ali Khan FL, Kubaib A, Imran PM, Nebbache N. Ternary Mixture of Pentanamide in Solvent Analogy with Halogenated Phenol: Experimental, Theoretical, and In Silico Biological Studies. ACS OMEGA 2023; 8:33928-33942. [PMID: 37744853 PMCID: PMC10515181 DOI: 10.1021/acsomega.3c04710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
This research describes the preparation of mixtures of new halogen-substituted phenol derivatives and their effects due to linkages with a fatty amide (pentanamide). The molecules were optimized using DFT, and the vibrational and electronic analysis was done subsequently. The energies of frontier molecular orbitals (FMOs) were used to estimate the global chemical reactivity parameters as we suggest that hydrogen-bonded networks may have contributed to the stability and reactivity of the compound. In addition to the experimental investigation, dielectric parameters were calculated. Fukui functions were analyzed to study the chemical reactivity. To get insight into interactions of σ → π* orbitals, natural bond orbital calculations were done. Additionally, surface analysis of the MEP and Hirshfeld charges were performed at the equivalent DFT levels. The research also indicated that both (interaction region indicator) IRI and (electron delocalize range) EDR would proficiently identify chemical-bonding and weak interaction regions, providing a significant advantage in exploring diverse chemical systems and reactions. This indicated that compounds could diffuse through noncovalent interactions, including intramolecular hydrogen bonding. Dielectric relaxation studies taken at five distinct molar ratios identified significant dielectric properties such as ε', ε″, ε0, and ε∞. The PA with FP, CP, BP, and IP molecules has potential antiviral and antioxidant benefits for carbonic anhydrase, with favorable drug-like features and diverse biological benefits. Pharmacological effects were forecasted using the PASS server, and these molecules exhibited favorable pharmacokinetic properties.
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Affiliation(s)
- A. Aathif Basha
- Department
of Physics, Islamiah College (Autonomous), Vaniyambadi 635752, Tamilnadu, India
| | - F. Liakath Ali Khan
- Department
of Physics, Islamiah College (Autonomous), Vaniyambadi 635752, Tamilnadu, India
| | - Attar Kubaib
- Department
of Chemistry, Islamiah College (Autonomous), Vaniyambadi 635752, Tamilnadu, India
| | | | - Nadia Nebbache
- Laboratory
of Applied Chemistry, University of Biskra, BP 145, 07000 Biskra, Algeria
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Thai NM, Dat TTH, Hai NTT, Bui TQ, Phu NV, Quy PT, Triet NT, Pham DT, De Tran V, Nhung NTA. Identification of potential inhibitors against Alzheimer-related proteins in Cordyceps militaris ethanol extract: experimental evidence and computational analyses. 3 Biotech 2023; 13:292. [PMID: 37547918 PMCID: PMC10403485 DOI: 10.1007/s13205-023-03714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023] Open
Abstract
Laboratory experiments were carried out to identify the chemical composition of Cordyceps militaris and reveal the first evidence of their Alzheimer-related potential. Liquid chromatography-mass spectrometry analysis identified 21 bioactive compounds in the ethanol extract (1-21). High-performance liquid chromatography quantified the content of cordycepin (0.32%). Bioassays revealed the overall anti-Alzheimer potential of the extract against acetylcholinesterase (IC50 = 115.9 ± 11.16 µg mL-1). Multi-platform computations were utilized to predict the biological inhibitory effects of its phytochemical components against Alzheimer-related protein structures: acetylcholinesterase (PDB-4EY7) and β-amyloid protein (PDB-2LMN). In particular, 7 is considered as a most effective inhibitor predicted by its chemical stability in dipole-based environments (ground state - 467.26302 a.u.; dipole moment 11.598 Debye), inhibitory effectiveness (DS ¯ - 13.6 kcal mol-1), polarized compatibility (polarizability 25.8 Å3; logP - 1.01), and brain penetrability (logBB - 0.244; logPS - 3.047). Besides, 3 is promising as a brain-penetrating agent (logBB - 0.257; logPS - 2.400). The results preliminarily suggest further experimental attempts to verify the pro-cognitive effects of l(-)-carnitine (7). Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03714-9.
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Affiliation(s)
- Nguyen Minh Thai
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000 Vietnam
| | - Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), Hue, 530000 Vietnam
| | - Nguyen Thi Thanh Hai
- Department of Chemistry, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Thanh Q. Bui
- Department of Chemistry, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Nguyen Vinh Phu
- Faculty of Basic Sciences, University of Medicine and Pharmacy, Hue University, Hue, 530000 Vietnam
| | - Phan Tu Quy
- Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000 Vietnam
| | - Nguyen Thanh Triet
- Faculty of Traditional Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000 Vietnam
| | - Duy Toan Pham
- Department of Chemistry, College of Natural Sciences, Can Tho University, Campus II, 3/2 Street, Can Tho, 900000 Vietnam
| | - Van De Tran
- Department of Health Organization and Management, Can Tho University of Medicine and Pharmacy, 179 Nguyen Van Cu, Can Tho, 900000 Vietnam
| | - Nguyen Thi Ai Nhung
- Department of Chemistry, University of Sciences, Hue University, Hue, 530000 Vietnam
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Castro-Velázquez V, Díaz-Cervantes E, Rodríguez-González V, Cortés-García CJ. In-silico assay of a dosing vehicle based on chitosan-TiO 2 and modified benzofuran-isatin molecules against Pseudomonas aeruginosa. PEERJ PHYSICAL CHEMISTRY 2023. [DOI: 10.7717/peerj-pchem.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
Abstract
A high priority of the World Health Organization (WHO) is the study of drugs against Pseudomonas aeruginosa, which has developed antibiotic resistance. In this order, recent research is analyzing biomaterials and metal oxide nanoparticles, such as chitosan (QT) and TiO2 (NT), which can transport molecules with biological activity against bacteria, to propose them as drug carrier candidates. In the present work, 10 modified benzofuran-isatin molecules were studied through computational simulation using density functional theory (DFT) and molecular docking assays against Hfq and LpxC (proteins of P. aeruginosa). The results show that the ligand efficiency of commercial drugs C-CP and C-AZI against Hfq is low compared with the best-designed molecule MOL-A. However, we highlight that the influence of NT promotes a better interaction of some molecules, where MOL-E generates a better interaction by 0.219 kcal/mol when NT is introduced in Hfq, forming the system Hfq-NT (Target-NT). Similar behavior is observed in the LpxC target, in which MOL-J is better at 0.072 kcal/mol. Finally, two pharmacophoric models for Hfq and LpxC implicate hydrophobic and aromatic-hydrophobic fragments.
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Affiliation(s)
- Verónica Castro-Velázquez
- División de Materiales Avanzados, Instituto Potosino de Investigación Científica y Tecnología, San Luis Potosí, San Luis Potosí, Mexico
- Departamento de Alimentos, Universidad de Guanajuato, Tierra Blanca, Guanajuato, Mexico
| | - Erik Díaz-Cervantes
- Departamento de Alimentos, Universidad de Guanajuato, Tierra Blanca, Guanajuato, Mexico
| | - Vicente Rodríguez-González
- División de Materiales Avanzados, Instituto Potosino de Investigación Científica y Tecnología, San Luis Potosí, San Luis Potosí, Mexico
| | - Carlos J. Cortés-García
- Laboratorio de Diseño Molecular/Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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Mhadhbi N, Dgachi S, Ben Ahmed A, Issaoui N, Nasr S, Badraoui R, Badraoui B, Naïli H. Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsonate Salt of 4-Aminopyridine. CHEMISTRY AFRICA 2023. [PMCID: PMC9926452 DOI: 10.1007/s42250-023-00620-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C5H7N2)(C5H8N2)[AsO4]·H2O ((4-APH)(4-APH2)[AsO4]·H2O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values.
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Affiliation(s)
- Noureddine Mhadhbi
- grid.412124.00000 0001 2323 5644Laboratory of Solid State, Department of Chemistry, Faculty of Sciences of Sfax, University of Sfax, B.P. N°1171, 3000 Sfax, Tunisia
| | - Souad Dgachi
- grid.412124.00000 0001 2323 5644Laboratory of Solid State, Department of Chemistry, Faculty of Sciences of Sfax, University of Sfax, B.P. N°1171, 3000 Sfax, Tunisia
| | - Ali Ben Ahmed
- grid.412124.00000 0001 2323 5644Laboratory of Applied Physics, Department of Physics, Faculty of Sciences of Sfax, University of Sfax, B.P. N°802, 3018 Sfax, Tunisia
| | - Noureddine Issaoui
- grid.411838.70000 0004 0593 5040Laboratory of Quantum and Statistical Physics, Department of Physics, Faculty of Sciences of Monastir, University of Monastir, 5079 Monastir, Tunisia
| | - Samia Nasr
- grid.442525.00000 0000 9284 9597Preparatory Institute for Engineering Studies Kairouan, Electrochemistry, Materials and Environment, University of Kairouan, Kairouan, Tunisia
| | - Riadh Badraoui
- grid.12574.350000000122959819Section of Histology-Cytology, Medicine Faculty of Tunis, University of Tunis El Manar, La Rabta, 1007 Tunis, Tunisia
| | - Bechir Badraoui
- grid.411838.70000 0004 0593 5040Research Unity of Materials and Et Organic Synthesis, Preparatory Institute for Engineering Studies of Monastir, University of Monastir, 5019 Monastir, Tunisia
| | - Houcine Naïli
- grid.412124.00000 0001 2323 5644Laboratory of Solid State, Department of Chemistry, Faculty of Sciences of Sfax, University of Sfax, B.P. N°1171, 3000 Sfax, Tunisia
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Shen H, Wang J, Ao J, Hou Y, Xi M, Cai Y, Li M, Luo A. Structure-activity relationships and the underlying mechanism of α-amylase inhibition by hyperoside and quercetin: Multi-spectroscopy and molecular docking analyses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121797. [PMID: 36115306 DOI: 10.1016/j.saa.2022.121797] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Inhibiting the activity of α-amylase has been considered an effective strategy to manage hyperglycemia. Hyperoside and quercetin are the main natural flavonoids in various plants, and the inhibition mechanism on α-amylase remains unclear. In this study, the structure-activity relationships between hyperoside/quercetin and α-amylase were evaluated by enzyme kinetic analysis, multi-spectroscopic techniques, and molecular docking analysis. Results showed that hyperoside and quercetin exhibited significant α-amylase inhibitory activities with IC50 values of 0.491 and 0.325 mg/mL, respectively. The α-amylase activity decreased in the presence of hyperoside and quercetin in a competitive and noncompetitive manner, respectively. UV-vis spectra suggested that the aromatic amino acid residues (Trp and Tyr) microenvironment of α-amylase changed in the presence of these two flavonoids. FTIR and CD spectra showed the vibrations of the amide bands and the secondary structure content changes. The fluorescence quenching mechanism of α-amylase by hyperoside and quercetin belonged to the static quenching type. Finally, molecular docking intuitively showed that hyperoside/quercetin formed hydrogen bonds with the key active site residues (Asp197, Glu233, and Asp300) in α-amylase. MD simulation indicated hyperoside/quercetin-α-amylase docked complexes had good stability. Taken together, this research provides new sights to developing potent drugs or functional foods with hyperoside and quercetin, offering new avenues for hyperglycemia treatment.
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Affiliation(s)
- Heyu Shen
- College of Food Science and Engineering, Northwest A&F University, Yangling, China.
| | - Jun Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China.
| | - Jingfang Ao
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yujie Hou
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Meihua Xi
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yingying Cai
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Mei Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Anwei Luo
- College of Food Science and Engineering, Northwest A&F University, Yangling, China.
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Experimental spectral investigations for structural, electronic, topological properties and molecular docking studies of 2-cyclohexylidene hydrazine carbaxamide. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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9
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Khanum G, Fatima A, Rather RA, Siddiqui N, Muthu S, Srivastava SK, Javed S. Synthesis, Spectroscopic, Quantum Chemical, and Molecular Docking Studies of 2-Cyano- N-Cyclopropylacetamide and 2-Cyano- N-(1-Phenylethyl)Acetamide. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2157452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ghazala Khanum
- S.O. S in Chemistry, Jiwaji University, Gwalior, MP, India
| | - Aysha Fatima
- S.O. S in Chemistry, Jiwaji University, Gwalior, MP, India
| | | | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, UP, India
| | - Sambanthan Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, India
| | | | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, UP, India
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10
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Abisha W, Dhas DA, Balachandran S, Joe IH. Synthesis, Structural, and Quantum Chemical Spectroscopic, Hydrogen Bonding, and Molecular Docking Investigation of Antifungal Compound Pyrazole-Pyrazolium Picrate. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2149571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- W. Abisha
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, India
- Manonmaniam Sundaranar University Abishekapatti, Tirunelveli, India
| | - D. Arul Dhas
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, India
- Manonmaniam Sundaranar University Abishekapatti, Tirunelveli, India
| | - S. Balachandran
- Department of Chemistry, NSS College Ottapalam, Palakkad, India
| | - I. Hubert Joe
- Department of Physics, Centre for Molecular and Biophysics Research, Mar Ivanios College, Thiruvanathapuram, India
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11
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Fizer O, Fizer M, Filep M, Sidey V, Mariychuk R. On the structure of cetylpyridinium perchlorate: A combined XRD, NMR, IR and DFT study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Thuy PT, Quan PM, Duc DX, Son NT. The antioxidative potential of procyanidin B1: DFT (density functional theory) and docking approaches. J Mol Model 2022; 28:356. [PMID: 36222929 DOI: 10.1007/s00894-022-05354-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/06/2022] [Indexed: 01/18/2023]
Abstract
Procyanidin B1 is one of the natural dimeric flavonoids. It has established a great role in antioxidative activity. In the current study, we wish to provide crucial information on its antioxidative action by the DFT computational and docking approaches. From point of thermodynamic view, at the M062X/6-311G(d,p) level, the HAT (hydrogen atom transfer) and SPL-ET (sequential proton loss-electron transfer) are principal antioxidative routes of this compound in gas and methanol, respectively. OH groups of two phenyl rings of this molecule are likely to be the best antiradical sites. In the kinetics of the interactions with HOO• radicals, OH groups of phenyl rings have also generated the best ΔG# (Gibbs free energy of activation) and rate constant K. The antioxidative action of procyanidin B1 is further confirmed by its chelation to metal ions, in which complex formation with Cu2+ having lower binding energy is more stable than complex formation with Zn2+. Docking study revealed that the antioxidative activity of procyanidin B1 involved human tyrosinase enzyme inhibition through interaction with essential residues, focusing on the OH groups of two phenyl rings.
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Affiliation(s)
- Phan Thi Thuy
- Faculty of Chemistry, College of Education, Vinh University, 182 Le Duan, Vinh, Nghean, Vietnam
| | - Pham Minh Quan
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam
| | - Dau Xuan Duc
- Faculty of Chemistry, College of Education, Vinh University, 182 Le Duan, Vinh, Nghean, Vietnam
| | - Ninh The Son
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam.
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Muthukumar R, Karnan M, Elangovan N, Karunanidhi M, Sankarapandian V, Thomas R. Synthesis, spectral, computational, wavefunction and molecular docking studies of 4-((thiophene-2-ylmethylene)amino)benzenesulfonamide from sulfanilamide and thiophene-2-carbalaldehyde. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Saeed A, Ejaz SA, Khalid A, Channar PA, Aziz M, Wani TA, Zargar S, Hassan S, Ismail H, Khalid D, Hashmi MZ, Hökelek T, Aborode AT. Facile synthesis, crystal structure, biological evaluation, and molecular modeling studies of N-((4-acetyl phenyl) carbamothioyl) pivalamide as the multitarget-directed ligand. Front Chem 2022; 10:992701. [PMID: 36226116 PMCID: PMC9549587 DOI: 10.3389/fchem.2022.992701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/22/2022] [Indexed: 01/18/2023] Open
Abstract
The crystal structure of N-((4-acetylphenyl)carbamothioyl)pivalamide (3) was synthesized by inert refluxing pivaloyl isothiocyanate (2) and 4-aminoacetophenone in dry acetone. The spectroscopic characterization (1H-NMR, 13CNMR, FT-IR) and single crystal assays determined the structure of synthesized compound (3). Systematic experimental and theoretical studies were conducted to determine the molecular characteristics of the synthesized crystal. The biological examination of (3) was conducted against a variety of enzymes i.e., acetyl cholinesterase (AChE), butyl cholinesterase (BChE), alpha amylase, and urease enzyme were evaluated. The crystal exhibited approximately 85% enzyme inhibition activity against BChE and AChE, but only 73.8 % and 57.9% inhibition activity against urease and alpha amylase was observed respectively. The theoretical calculations were conducted using density functional theory studies (DFTs) with the 6–31G (d, p) basis set and B3LYP functional correlation. The Frontier molecular orbital analysis revealed that the HOMO/LUMO energy gap was smaller, which corresponds to the molecule’s reactivity. In terms of reactivity, the chemical softness value was found to be in good agreement with experimental values. In Crystal structure analysis, the intramolecular N—H•••O hydrogen bond generates a S 6) ring motif and N—H•••O interactions exist in crystal structure between the centroids of neighboring parallel aromatic (C4-C9) rings with a centroid to centroid distance of 3.9766 (7)Å. These intermolecular interactions were useful in structural stabilization. The Hirshfeld surfaces and their related two-dimensional fingerprint plots were used for thorough investigation of intermolecular interactions. According to Hirshfeld surface analysis of the crystal structure the most substantial contributions to the crystal packing are from H ••• O and H ••• N/N ••• H interactions. Molecular docking studies were conducted to evaluate the binding orientation of synthesized crystal with multiple targets. The compound exhibited stronger interactions with AChE and BChE with binding energies of -7.5 and -7.6 kcal/mol, respectively. On the basis of in-vitro and in-silico findings, it is deduced that N-((4-acetylphenyl)carbamothioyl)pivalamide 3) possesses reactive and potent multiple target inhibitory properties.
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Affiliation(s)
- Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
- *Correspondence: Aamer Saeed, , , Syeda Abida Ejaz, ,
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- *Correspondence: Aamer Saeed, , , Syeda Abida Ejaz, ,
| | - Aqsa Khalid
- Department of Chemistry, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Pervaiz Ali Channar
- Department of Chemistry, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
- Department of Basic Sciences, Mathematics and Humanities, Dawood University of Engineering and Technology, Karachi, Pakistan
| | - Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Tanveer A. Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Seema Zargar
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sidra Hassan
- Bahawalpur College of Pharmacy, Bahawalpur Medical and Dental College, Bahawalpur, Pakistan
| | - Hammad Ismail
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Dania Khalid
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
| | | | - Tuncer Hökelek
- Department of Physics, Faculty of Engineering, Hacettepe University, Ankara, Turkey
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Feride Akman, Kazachenko AS, Issaoui N. DFT Calculations of Some Important Radicals Used in the Nitroxide-Mediated Polymerization and Their HOMO‒LUMO, Natural Bond Orbital, and Molecular Electrostatic Potential Comparative Analysis. POLYMER SCIENCE SERIES B 2022. [DOI: 10.1134/s156009042270035x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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16
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Feride Akman, Kazachenko AS, Issaoui N. DFT Calculations of Some Important Radicals Used in the Nitroxide-Mediated Polymerization and Their HOMO‒LUMO, Natural Bond Orbital, and Molecular Electrostatic Potential Comparative Analysis. POLYMER SCIENCE SERIES B 2022. [DOI: doi.org/10.1134/s156009042270035x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Ramalingam A, Guerroudj AR, Sambandam S, Kumar A, Krishnamoorthy R, Boukabcha N, Chouaih A, Manikandan E. Synthesis, vibrational spectra, Hirshfeld surface analysis, DFT calculations, and in silico ADMET study of 3-(2-chloroethyl)-2,6-bis(4-fluorophenyl)piperidin-4-one: A potent anti-Alzheimer agent. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Van Chen T, Cuong TD, Quy PT, Bui TQ, Van Tuan L, Van Hue N, Triet NT, Ho DV, Bao NC, Nhung NTA. Antioxidant activity and α-glucosidase inhibitability of Distichochlamys citrea M.F. Newman rhizome fractionated extracts: in vitro and in silico screenings. CHEMICAL PAPERS 2022; 76:5655-5675. [PMID: 35669698 PMCID: PMC9159386 DOI: 10.1007/s11696-022-02273-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/09/2022] [Indexed: 01/18/2023]
Abstract
Distichochlamys citrea M.F. Newman (commonly known as “Black Ginger”) is an endemic plant to Vietnam and has been extensively exploited by folk medication for treatments of infection-related diseases and diabetes. In this work, its rhizomes were subjected to fractionated extraction, phytochemical examination, evaluation of antioxidant effect by DDPH free radical neutralization, and inhibitory activity toward α-glucosidase. The compositional components were subjected to in silico screening, including density functional theory calculation, molecular docking simulation, physicochemical analysis, and pharmacokinetic regression. In the trials, EtOAc fraction is found as the bioactive part of most effectiveness, regarding both antioxidant effect (IC50 = 90.27 µg mL−1) and α-glucosidase inhibitory activity (IC50 = 115.75 μg mL−1). Chemical determination reveals there are 13 components of its composition. DFT-based calculations find no abnormal constraints in their structures. Docking-based simulation provides order of inhibitory effectiveness: 3-P53341 > 12-P53341 > 7-P53341 > 4-P53341 > 11-P53341 > 10-P53341. QSARIS-based investigations implicate their biocompatibility. ADMET-based regressions indicate that all candidates are generally safe for medicinal applications. The findings would contribute to the basis for further studies on the chemical compositions of Distichochlamys citrea and their biological activities.
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Affiliation(s)
- Tran Van Chen
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000 Vietnam
| | - To Dao Cuong
- Phenikaa University Nano Institute (PHENA), Phenikaa University, Yen Nghia, Ha Dong District, Hanoi, 12116 Vietnam
| | - Phan Tu Quy
- Department of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot, 630000 Vietnam
| | - Thanh Q. Bui
- Department of Chemistry, University of Sciences, Hue University, Hue City, 530000 Vietnam
| | - Le Van Tuan
- Department of Environmental Science, University of Sciences, Hue University, Hue City, 530000 Vietnam
| | - Nguyen Van Hue
- Faculty of Engineering and Food Technology, University of Agriculture and Forestry, Hue University, Hue City, 530000 Vietnam
| | - Nguyen Thanh Triet
- Faculty of Traditional Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000 Vietnam
| | - Duc Viet Ho
- Faculty of Pharmacy, Hue University of Medicine and Pharmacy, Hue University, Hue City, 530000 Vietnam
| | | | - Nguyen Thi Ai Nhung
- Department of Chemistry, University of Sciences, Hue University, Hue City, 530000 Vietnam
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19
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Rbaa M, Mequedade M, Berkiks I, Lakhrissi Y, Mague J, El Hessni A, Hadda TB, Warad I, Lakhrissi B, Zarrouk A. Toxicological and Pharmacological Studies of a Crystal Structure Derivative of 8-Hydroxyquinoline. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-021-06007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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20
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Bravanjalin Subi E, Arul Dhas D, Balachandran S, Hubert Joe I. Crystal Growth, Structural, Vibrational, Effects of Hydrogen Bonding(C-H…O and C-H…N), Chemical Reactivity, Antimicrobial Activity, Inhibitory Effects and Molecular Dynamic Simulation of 4-Methoxy-N-(Nitrobenzylidene)-Aniline. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2052116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- E. Bravanjalin Subi
- Manonmaniam Sundaranar University, Abishekapatti, Tirunelveli, Tamil Nadu, India
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, Tamil Nadu, India
| | - D. Arul Dhas
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, Tamil Nadu, India
| | - S. Balachandran
- Department of Chemistry, NSS College Ottapalam, Palakad, Kerala, India
| | - I. Hubert Joe
- Centre for Molecular and Biophysics Research, Department of Physics, Mar Ivanios College, Thiruvanathapuram, Kerala, India
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21
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Van Hue N, Cuong TD, Quy PT, Bui TQ, Hai NTT, Triet NT, Thanh DD, Nhi NTT, Thai NM, Van Chen T, Nhung NTA. Antimicrobial Properties of
Distichochlamys citrea
M.F. Newman Rhizome
n
‐Hexane Extract against
Streptococcus pyogenes
: Experimental Evidences and Computational Screening. ChemistrySelect 2022. [DOI: 10.1002/slct.202200680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Nguyen Van Hue
- Faculty of Engineering and Food Technology University of Agriculture and Forestry Hue University Hue City 530000 Vietnam
| | - To Dao Cuong
- Phenikaa University Nano Institute (PHENA) Phenikaa University, Yen Nghia, Ha Dong District Hanoi 12116 Vietnam
| | - Phan Tu Quy
- Department of Natural Sciences & Technology Tay Nguyen University Buon Ma Thuot 630000 Vietnam
| | - Thanh Q. Bui
- Department of Chemistry University of Sciences Hue University Hue City 530000 Vietnam
| | - Nguyen Thi Thanh Hai
- Department of Chemistry University of Sciences Hue University Hue City 530000 Vietnam
| | - Nguyen Thanh Triet
- Faculty of Traditional Medicine University of Medicine and Pharmacy Ho Chi Minh City 700000 Vietnam
| | - Doan Duy Thanh
- Navetco National Veterinary Joint Stock Company Ho Chi Minh City 700000 Vietnam
| | - Nguyen Thanh To Nhi
- Faculty of Pharmacy Nguyen Tat Thanh University Ho Chi Minh City 700000 Vietnam
| | - Nguyen Minh Thai
- Faculty of Pharmacy University of Medicine and Pharmacy Ho Chi Minh City 700000 Vietnam
| | - Tran Van Chen
- Faculty of Pharmacy University of Medicine and Pharmacy Ho Chi Minh City 700000 Vietnam
| | - Nguyen Thi Ai Nhung
- Department of Chemistry University of Sciences Hue University Hue City 530000 Vietnam
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22
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Sangeetha P, Sangeetha R, Mullainathan S, Irfan A, Sevvanthi S, Muthu S. Molecular docking evaluation and spectroscopic study of 2-amino-1,4-benzenedisulfonic acid using the IEFPCM model, electronic properties of different solvents. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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23
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Experimental and theoretical investigations on structural-function relationship of new iron (III) complex with 2-(Ammoniomethyl)pyridinium cation as ligand: A promising material for green solar cells. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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24
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Modelling the DFT structural and reactivity study of feverfew and evaluation of its potential antiviral activity against COVID-19 using molecular docking and MD simulations. CHEMICAL PAPERS 2022; 76:2759-2776. [PMID: 35068663 PMCID: PMC8760597 DOI: 10.1007/s11696-022-02067-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/05/2022] [Indexed: 01/18/2023]
Abstract
Abstract The unavailability of a proper drug against SARS-CoV-2 infections and the emergence of various variants created a global crisis. In the present work, we have studied the antiviral behavior of feverfew plant in treating COVID-19. We have reported a systematic in silico study with the antiviral effects of various phytoconstituents Borneol (C10H18O), Camphene (C10H16), Camphor (C10H16O), Alpha-thujene (C10H16), Eugenol (C10H14O), Carvacrol (C10H14O) and Parthenolide (C15H20O3) of feverfew on the viral protein of SARS-CoV-2. Parthenolide shows the best binding affinity with both main protease (Mpro) and papain-like protease (PLpro). The molecular electrostatic potential and Mulliken atomic charges of the Parthenolide molecule shows the high chemical reactivity of the molecule. The docking of Parthenolide with PLpro give score of −8.0 kcal/mol that validates the good binding of Parthenolide molecule with PLpro. This complex was further considered for molecular dynamics simulations. The binding energy of the complex seems to range in between −3.85 to −11.07 kcal/mol that is high enough to validate the stability of the complex. Free energy decomposition analysis have been also performed to understand the contribution of residues that reside into the binding site. Good binding affinity and reactivity response suggested that Parthenolide can be used as a promising drug against the COVID-19. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11696-022-02067-6.
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25
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Theoretical electron excitation study in liquid phase (protic, aprotic, non-polar) and inter and intra molecular reactivity of 2-hydroxy-5-[1-hydroxy-2-(4-phenylbutan-2-ylamino) ethyl] benzamide. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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26
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Amalanathan M, Michael Mary MS, Beatrice ML, Delphine SM, Robert HM, Twinkle AR, Ratkovic Z, Samson Y. Synthesis, structural, spectroscopic and docking studies on (E)-1-Ferrocenyl-3-phenylpropen-1-one by the density functional theory. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.2016743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- M. Amalanathan
- Department of Physics & Research Centre, Nanjil Catholic College of Arts and Science, Kaliyakkavilai, India
| | - M. Sony Michael Mary
- Manonmaniam Sundaranar University, Tirunelveli, India
- Department of Physics & Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - M. Latha Beatrice
- Manonmaniam Sundaranar University, Tirunelveli, India
- Department of Physics & Research Centre, Holy Cross College, Nagercoil, India
| | - S. Mary Delphine
- Department of Physics & Research Centre, Holy Cross College, Nagercoil, India
| | - H. Marshan Robert
- Department of Physics & Research Centre, Women’s Christian College, Nagercoil, India
| | - A. R. Twinkle
- Department of Physics, Mar Ivanios College, Thiruvananthapuram, India
| | - Zoran Ratkovic
- Department of Chemistry, Faculty of Science, University of Kragujevac, Kragujevac, Serbia
| | - Y. Samson
- Department of Physics, Annai Velankanni College, Tholayavattan, India
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27
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Yadav P, Rana M, Chowdhury P. DFT and MD simulation investigation of favipiravir as an emerging antiviral option against viral protease (3CL pro) of SARS-CoV-2. J Mol Struct 2021; 1246:131253. [PMID: 34376872 PMCID: PMC8342190 DOI: 10.1016/j.molstruc.2021.131253] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 01/18/2023]
Abstract
As per date, around 20 million COVID-19 cases reported from across the globe due to a tiny 125 nm sized virus: SARS-CoV-2 which has created a pandemic and left an unforgettable impact on our world. Besides vaccine, medical community is in a race to identify an effective drug, which can fight against this disease effectively. Favipiravir (F) has recently attracted too much attention as an effective repurposed drug against COVID-19. In the present study, the pertinency of F has been tested as an antiviral option against viral protease (3CLpro) of SARS-CoV-2 with the help of density functional theory (DFT) and MD Simulation. Different electronic properties of F such as atomic charges, molecular electrostatic properties (MEP), chemical reactivity and absorption analysis have been studied by DFT. In order to understand the interaction and stability of inhibitor F against viral protease, molecular docking and MD simulation have been performed. Various output like interaction energies, number of intermolecular hydrogen bonding, binding energy etc. have established the elucidate role of F for the management of CoV-2 virus for which there is no approved therapies till now. Our findings highlighted the need to further evaluate F as a potential antiviral against SARS-CoV-2.
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Affiliation(s)
- Pooja Yadav
- Department of Physics and Materials Science and Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh 201309, India
| | - Meenakshi Rana
- Department of Physics, School of Sciences, Uttarakhand Open University, Haldwani, Uttarakhand 263139, India
| | - Papia Chowdhury
- Department of Physics and Materials Science and Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh 201309, India
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28
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Vimala M, Stella Mary S, Ramalakshmi R, Muthu S, Niranjana Devi R, Irfan A. Quantum computational studies on optimization, donor-acceptor analysis and solvent effect on reactive sites, global descriptors, non-linear optical parameters of Methyl N-Boc-piperidine-3-carboxylate. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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29
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Medimagh M, Issaoui N, Gatfaoui S, Al-Dossary O, S. Kazachenko A, Marouani H, Wojcik M. Molecular modeling and biological activity analysis of new organic-inorganic hybrid: 2-(3,4-dihydroxyphenyl) ethanaminium nitrate. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2021. [DOI: 10.1016/j.jksus.2021.101616] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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30
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Probing solvent effect and strong and weak interactions in 2-Nitrophenyl-hydrazine using independent gradient model and Hirshfeld from wave function calculation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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31
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Jeelani A, Muthu S, Narayana B. Molecular structure determination, Bioactivity score, Spectroscopic and Quantum computational studies on (E)-N'-(4-Chlorobenzylidene)-2-(napthalen-2-yloxy) acetohydrazide. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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32
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Medimagh M, Issaoui N, Gatfaoui S, Antonia Brandán S, Al-Dossary O, Marouani H, J. Wojcik M. Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and molecular docking study. Heliyon 2021; 7:e08204. [PMID: 34754970 PMCID: PMC8556648 DOI: 10.1016/j.heliyon.2021.e08204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/09/2021] [Accepted: 10/14/2021] [Indexed: 01/18/2023] Open
Abstract
In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease.
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Affiliation(s)
- Mouna Medimagh
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir, 5079, Tunisia
| | - Noureddine Issaoui
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir, 5079, Tunisia
| | - Sofian Gatfaoui
- University of Carthage, Laboratory of Chemistry of Materials (LR13ES08), Faculty of Sciences of Bizerte, 7021, Tunisia
| | - Silvia Antonia Brandán
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, San Miguel de Tucumán, Tucumán, Argentina
| | - Omar Al-Dossary
- Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | - Houda Marouani
- University of Carthage, Laboratory of Chemistry of Materials (LR13ES08), Faculty of Sciences of Bizerte, 7021, Tunisia
| | - Marek J. Wojcik
- Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Gronostajowa 2, Poland
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33
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Ben Khemis I, Sagaama A, Issaoui N, Ben Lamine A. Steric and energetic characterizations of mouse and human musk receptors activated by nitro musk smelling compounds at molecular level: Statistical physics treatment and molecular docking analysis. Int J Biol Macromol 2021; 188:333-342. [PMID: 34389381 DOI: 10.1016/j.ijbiomac.2021.08.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/12/2021] [Accepted: 08/05/2021] [Indexed: 01/18/2023]
Abstract
Understanding olfaction process at a microscopic or molecular level needs more elucidation of the multiple stages involved in the olfaction mechanism. A worth full elucidation and a better understanding of this molecular mechanism, a necessary preamble should be achieved. The content of this work is a preamble for that. A study of the mouse and human olfactory receptors activation in response to two nitro musks stimuli, which are the musk xylol and the musk ketone, are considered here, first, for their wide expanded use in perfumery, but also to show some particular aspects of this process in the case of these two stimuli, which could help to deduce more details and more general aspects in the global olfactory mechanism. A statistical physics modeling using the monolayer model with two independent types of receptor binding sites of the response of the mouse olfactory receptor MOR215-1 and the human olfactory receptor OR5AN1, which are identified as specifically responding to musk compounds, is used to characterize the interaction between the two nitro musk molecules, the mouse and the human olfactory receptors and to determine the olfactory band of these two odorants through the determination of the molar adsorption energies and the adsorption energy distributions. The physico-chemical model parameters can be used for the steric characterization via the calculation of the receptor site size distributions. The docking computation between these two nitro musks and the human olfactory receptor OR5AN1 is performed demonstrating a large similarity in receptor-ligand detection process. Thus, docking finding results prove that the calculated binding affinities were belonging to the spectrum of adsorption energies.
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Affiliation(s)
- Ismahene Ben Khemis
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia.
| | - Abir Sagaama
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia
| | - Noureddine Issaoui
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia
| | - Abdelmottaleb Ben Lamine
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia.
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Structural (monomer and dimer), wavefunctional, NCI analysis in aqueous phase, electronic and excited state properties in different solvent atmosphere of 3-{(E)-[(3,4-dichlorophenyl)imino]methyl} benzene-1,2-diol. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116335] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Carbazole derivatives: Synthesis, spectroscopic characterization, antioxidant activity, molecular docking study, and the quantum chemical calculations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115651] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Quantum chemical calculations, spectroscopic properties and molecular docking studies of a novel piperazine derivative. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2021. [DOI: 10.1016/j.jksus.2020.101283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Noureddine O, Issaoui N, Medimagh M, Al-Dossary O, Marouani H. Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations. JOURNAL OF KING SAUD UNIVERSITY SCIENCE 2021; 33:101334. [PMID: 33432258 PMCID: PMC7787522 DOI: 10.1016/j.jksus.2020.101334] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 01/18/2023]
Abstract
Structure-activity relationships for hydroxychloroquine compound and its derivatives resulted in a potent antiviral activity. Where hydroxychloroquine derivatives showed an apparent efficacy against coronavirus related pneumonia. For this reason, the current study is focused on the structural properties of hydroxychloroquine and hydroxychloroquine sulfate. Optimized structures of these molecules have been reported by using DFT method at B3LYP/6-31G* level of theory. The geometric were determined and compared with the experimental crystal structure. The intra and intermolecular interactions which exist within these compounds are analyzed by different methods namely the topological analysis AIM, ELF and the reduced gradient of the density. These approaches make it possible in particular to study the properties of hydrogen bonds. The highest occupied molecular orbital and the lowest unoccupied molecular orbital energy levels are constructed and the corresponding frontier energy gaps are determined to realize the charge transfer within the molecule. The densities of state diagrams were determined to calculate contributions to the molecular orbitals. The molecular electrostatic potential surfaces are determined to give a visual representation of charge distribution of these ligands and to provide information linked to electrophilic and nucleophilic sites localization. Finally, these derivatives were evaluated for the inhibition of COVID-19 activity by using the molecular docking method.
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Affiliation(s)
- Olfa Noureddine
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Noureddine Issaoui
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Mouna Medimagh
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Omar Al-Dossary
- Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Houda Marouani
- University of Carthage, Laboratory of Chemistry of Materials (LR13ES08), Faculty of Sciences of Bizerte, 7021, Tunisia
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Kazachenko AS, Akman F, Sagaama A, Issaoui N, Malyar YN, Vasilieva NY, Borovkova VS. Theoretical and experimental study of guar gum sulfation. J Mol Model 2021; 27:5. [PMID: 33389146 DOI: 10.1007/s00894-020-04645-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/10/2020] [Indexed: 01/18/2023]
Abstract
The synthesis of guar gum sulfates by a complex of sulfur trioxide with 1,4-dioxane was studied. The influence of temperature, process duration, and the volume of chlorosulfonic acid on the degree of substitution of guar gum sulfates was studied. The sulfation process has been optimized using the Box-Behnken design. It was shown that the optimal conditions for sulfation of guar gum with a complex of sulfur trioxide-1.4-dioxane: temperature 60 °C, duration 2.9 h, and a volume of chlorosulfonic acid of 3.1 ml. Sulfate groups embedding into the structure of guar gum was confirmed by elemental analysis and FTIR. The initial and sulfated guar gum were also characterized by methods: X-ray diffraction, scanning electron microscopy, and gel permeation chromatography. Using X-ray diffraction, it was shown that amorphization of guar gum occurs during sulfation. Using scanning electron microscopy, it was shown that the morphology of guar gum changes in the process of sulfation. Using gel permeation chromatography, it was shown in the process of guar gum sulfation by a complex of sulfur trioxide with 1,4-dioxane, the molecular weight decreases from 600 to 176 kDa. The geometric parameters of all complexes were carried out by using the DFT/B3PW91 method with a 6-31 + G (d,p) basis set. These structures are optimized to predict the important properties of a theme. MEP with contour map has been performed to obtain the electronic properties. Frontier molecular orbital HOMO-LUMO orbital diagram has been obtained for different energy levels and their band gap energies have been computed.
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Affiliation(s)
- Aleksandr S Kazachenko
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok, 50/24, Krasnoyarsk, Russia, 660036. .,Siberian Federal University, Svobodny av., 79, Krasnoyarsk, Russia, 660041.
| | - Feride Akman
- Vocational School of Technical Sciences, University of Bingöl, 12000, Bingol, Turkey
| | - Abir Sagaama
- Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, University of Monastir, 5079, Monastir, Tunisia
| | - Noureddine Issaoui
- Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, University of Monastir, 5079, Monastir, Tunisia
| | - Yuriy N Malyar
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok, 50/24, Krasnoyarsk, Russia, 660036.,Siberian Federal University, Svobodny av., 79, Krasnoyarsk, Russia, 660041
| | - Natalya Yu Vasilieva
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok, 50/24, Krasnoyarsk, Russia, 660036.,Siberian Federal University, Svobodny av., 79, Krasnoyarsk, Russia, 660041
| | - Valentina S Borovkova
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok, 50/24, Krasnoyarsk, Russia, 660036.,Siberian Federal University, Svobodny av., 79, Krasnoyarsk, Russia, 660041
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Noureddine O, Issaoui N, Al-Dossary O. DFT and molecular docking study of chloroquine derivatives as antiviral to coronavirus COVID-19. JOURNAL OF KING SAUD UNIVERSITY SCIENCE 2020; 33:101248. [PMID: 33250604 PMCID: PMC7687412 DOI: 10.1016/j.jksus.2020.101248] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 01/18/2023]
Abstract
The recently emerged COVID-19 virus caused hundreds of thousands of deaths and instigated a widespread fear, threatening the world’s most advanced health security. In 2020, chloroquine derivatives are among the drugs tested against the coronavirus pandemic and showed an apparent efficacy. In the present work, the chloroquine and the chloroquine phosphate molecules have been proposed as potential antiviral for the treatment of COVID-19 diseases combining DFT and molecular docking calculations. Molecular geometries, electronic properties and molecular electrostatic potential were investigated using density functional theory (DFT) at the B3LYP/6-31G* method. As results, we found a good agreement between the theoretical and the experimental geometrical parameters (bond lengths and bond angles). The frontier orbitals analysis has been calculated at the same level of theory to determine the charge transfer within the molecule. In order to perform a better description of the FMOs, the density of states was determined. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of molecule and also to describe the intermolecular interactions. All these studies help us a lot in determining the reactivity of the mentioned compounds. Finally, docking calculations were carried out to determine the pharmaceutical activities of the chloroquine derivatives against coronavirus diseases. The choice of these ligands was based on their antiviral activities.
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Affiliation(s)
- Olfa Noureddine
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Noureddine Issaoui
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Omar Al-Dossary
- Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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