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Shen Y, Duan H, Yuan L, Asikaer A, Liu Y, Zhang R, Liu Y, Wang Y, Lin Z. Computational biology-based study of the molecular mechanism of spermidine amelioration of acute pancreatitis. Mol Divers 2023:10.1007/s11030-023-10698-4. [PMID: 37523101 DOI: 10.1007/s11030-023-10698-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
Acute pancreatitis (AP) is an acute inflammatory gastrointestinal disease, the mortality and morbility of which has been on the increase in the past years. Spermidine, a natural polyamine, has a wide range of pharmacological effects including anti-inflammation, antioxidation, anti-aging, and anti-tumorigenic. This study aimed to investigate the reliable targets and molecular mechanisms of spermidine in treating AP. By employing computational biology methods including network pharmacology, molecular docking, and molecular dynamics (MD) simulations, we explored the potential targets of spermidine in improving AP with dietary supplementation. The computational biology results revealed that spermidine had high degrees (degree: 18, betweenness: 38.91; degree: 18, betweenness: 206.41) and stable binding free energy (ΔGbind: - 12.81 ± 0.55 kcal/mol, - 15.00 ± 1.00 kcal/mol) with acetylcholinesterase (AchE) and serotonin transporter (5-HTT). Experimental validation demonstrates that spermidine treatment could reduce the necrosis and AchE activity in pancreatic acinar cells. Cellular thermal shift assay (CETSA) results revealed that spermidine could bind to and stabilize the 5-HTT protein in acinar cells. Moreover, spermidine treatment impeded the rise of the expression of 5-HTT in pancreatic tissues of caerulein induced acute pancreatitis mice. In conclusion, serotonin transporter might be a reliable target of spermidine in treating AP. This study provides new idea for the exploration of potential targets of natural compounds.
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Affiliation(s)
- Yan Shen
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, People's Republic of China
| | - Hongtao Duan
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Lu Yuan
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Aiminuer Asikaer
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Yiyuan Liu
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Yang Liu
- Department of Hepatobiliary Surgery II, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Yuanqiang Wang
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, People's Republic of China
| | - Zhihua Lin
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, People's Republic of China.
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2
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Duan H, Zhang R, Yuan L, Liu Y, Asikaer A, Liu Y, Shen Y. Exploring the therapeutic mechanisms of Gleditsiae Spina acting on pancreatic cancer via network pharmacology, molecular docking and molecular dynamics simulation. RSC Adv 2023; 13:13971-13984. [PMID: 37181515 PMCID: PMC10167735 DOI: 10.1039/d3ra01761c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/19/2023] [Indexed: 05/16/2023] Open
Abstract
Pancreatic cancer is one of the most aggressive tumors and also has a low survival rate. The dried spines of Gleditsia sinensis Lam are known as "Gleditsiae Spina" and they mostly contain flavonoids, phenolic acids, terpenoids, steroids, and other chemical components. In this study, the potential active components and molecular mechanisms of Gleditsiae Spina for treating pancreatic cancer were systematically revealed by network pharmacology, molecular docking and molecular dynamics simulations (MDs). RAC-alpha serine/threonine-protein kinase (AKT1), cellular tumor antigen p53 (TP53), tumor necrosis factor α (TNFα), interleukin-6 (IL6) and vascular endothelial growth factor A (VEGFA) were common targets of Gleditsiae Spina, human cytomegalovirus infection signaling pathway, AGE-RAGE signaling pathway in diabetic complications, and MAPK signaling pathway were critical pathways of fisetin, eriodyctiol, kaempferol and quercetin in the treatment of pancreatic cancer. Molecular dynamics simulations (MDs) results showed that eriodyctiol and kaempferol have long-term stable hydrogen bonds and high binding free energy for TP53 (-23.64 ± 0.03 kcal mol-1 and -30.54 ± 0.02 kcal mol-1, respectively). Collectively, our findings identify active components and potential targets in Gleditsiae Spina for the treatment of pancreatic cancer, which may help to explore leading compounds and potential drugs for pancreatic cancer.
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Affiliation(s)
- Hongtao Duan
- School of Pharmacy and Bioengineering, Chongqing University of Technology Chongqing 405400 China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital 550002 Guiyang China
| | - Lu Yuan
- School of Pharmacy and Bioengineering, Chongqing University of Technology Chongqing 405400 China
| | - Yiyuan Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology Chongqing 405400 China
| | - Aiminuer Asikaer
- School of Pharmacy and Bioengineering, Chongqing University of Technology Chongqing 405400 China
| | - Yang Liu
- Department of Hepatobiliary Surgery II, Guizhou Provincial People's Hospital 550002 Guiyang China
| | - Yan Shen
- School of Pharmacy and Bioengineering, Chongqing University of Technology Chongqing 405400 China
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3
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Effect of caffeic acid esters on antioxidant activity and oxidative stability of sunflower oil: Molecular simulation and experiments. Food Res Int 2022; 160:111760. [DOI: 10.1016/j.foodres.2022.111760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 12/26/2022]
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4
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Rajesh R, Muthu S, Sheela N. Investigations of 6-Fluoro-4-Oxo-3,4-Dihydro-2H-Chromene-2-Carboxylic Acid by Quantum Computational, Spectroscopic, TD-DFT with Various Solvents and Molecular Docking Studies. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2124284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- R. Rajesh
- Department of Physics, Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College (Autonomous), Chennai, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, India
| | - N.R. Sheela
- Department of Applied Physics, Sri Venkateswara College of Engineering (Autonomous), Chennai, India
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E. E, Prasana JC, Muthu S, Anuradha A. Molecular Structure, Spectroscopic, Quantum Computational, and Molecular Docking Investigations on Propyl Gallate. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2107688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Eunice E.
- Department of Physics, Madras Christian College, East Tambaram, Tamil Nadu, India
- University of Madras, Chennai, Tamil Nadu, India
| | - Johanan Christian Prasana
- Department of Physics, Madras Christian College, East Tambaram, Tamil Nadu, India
- University of Madras, Chennai, Tamil Nadu, India
| | - S. Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, Tamil Nadu, India
- Department of Physics, Puratchi Thalaivar Dr. M. G. R Government Arts and Science College, Uthiramerur, Tamil Nadu, India
| | - A. Anuradha
- University of Madras, Chennai, Tamil Nadu, India
- PG & Research Department of Physics, Queen Mary’s College, Chennai, Tamil Nadu, India
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6
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Tariq S, Mutahir S, Khan MA, Mutahir Z, Hussain S, Ashraf M, Bao X, Zhou B, Stark CB, Khan IU. Synthesis, in vitro cholinesterase inhibition, molecular docking, DFT and ADME studies of novel 1,3,4-oxadiazole 2-thiol derivatives. Chem Biodivers 2022; 19:e202200157. [PMID: 35767725 DOI: 10.1002/cbdv.202200157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/29/2022] [Indexed: 11/11/2022]
Abstract
A sequence of 1,3,4-oxadiazole 2-thiol derivatives bearing various alkyl or aryl moieties was designed, synthesized, and characterized by modern spectroscopic methods to yield 17 compounds ( 6a - 6q ) which were screened for acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes in search of 'lead' compounds for the treatment of Alzheimer disease (AD). The compounds 6q, 6p, 6k, 6o, and 6l showed inhibitory capability against AChE and BChE, with IC 50 values ranging from 11.730.49 to 27.360.29 µM for AChE and 21.830.39 to 39.430.44 µM for BChE, inhibiting both enzymes within a limited range. The SAR ascertained that the substitution of the aromatic moiety had a profound effect on the AChE and BChE inhibitory potential as compared to the aliphatic substitutions which were supported by the molecular docking studies. In silico ADME studies reinforced the drug-likeness of most of the synthesized molecules. These results were additionally supplemented by the molecular orbital analysis (HOMO-LUMO) and electrostatic potential maps got from DFT calculations. ESP maps expose that on all structures, there are two potential binding sites conquered by the most positive and most negative districts.
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Affiliation(s)
- Sidrah Tariq
- Government College University Lahore, Department of Chemitry, Anarkaly Lahore, 54000, Lahore, PAKISTAN
| | - Sadaf Mutahir
- University of Sialkot, Department of Chemitry, Daska Road Sialkot, Sialkot, PAKISTAN
| | - Muhammad Asim Khan
- Nanjing University of Science and Technology, School of Chemical Engineering, Xiaolingwei 200, Nanjing 210094, 210000, China, 210000, Nanjing, CHINA
| | - Zeeshan Mutahir
- University of the Punjab Quaid-i-Azam Campus: University of the Punjab, Institute of Biochemistry and Biotechnology, University of the Punjab, 54590 Lahore, Pakistan, Lahore, PAKISTAN
| | - Safdar Hussain
- Islamia University: The Islamia University of Bahawalpur Pakistan, Department of Chemitry, Bahwalpur, Bahwalpur, PAKISTAN
| | - Muhammad Ashraf
- Islamia University: The Islamia University of Bahawalpur Pakistan, Department of Chemitry, Bahwalpur, Government College University Lahore, 54000, Bahwalpur, PAKISTAN
| | - Xiaofang Bao
- Nanjing University of Science and Technology, School of Chemical Engineering, Room No. 104. 2nd Old Chemical Building, School of Chemical Engineering, 210094, 210094, Nanjing, CHINA
| | - Baojing Zhou
- Nanjing University of Science and Technology, School of Chemical Engineering, Room No. 104. 2nd Old Chemical Building, School of Chemical Engineering, 210094, 210094, Nanjing, CHINA
| | - Christian Bw Stark
- Universitat Hamburg Zentralbibliothek Recht: Universitat Hamburg, Fachbereich Chemie, Institut für Organische Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany, Hamburg, GERMANY
| | - Islam Ullah Khan
- University of Mianwali, Department of Chemistry/VC Office, VC Office, Department of Chemistry, University of Mianwali, Pakistan, Mianwali, PAKISTAN
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Upendranath K, Venkatesh T, Shashank M, Nagaraju G, Pasha KMM. One-pot synthesis of some new 7‑hydroxy-5-(4-substitutedphenyl)-9-methyl-1,5-dihydro-2H-dipyrimido[1,2-a:4′,5′-d]pyrimidine-2,4(3H)‑dione derivatives and it's optoelectronic, DFT, photocatalytic studies and latent fingerprint applications. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Structural, spectroscopic, and in silico studies of 3-(dimethylamino)-1-(thiophen-2-yl)propan-1-ol: A potential antidepressant agent. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Spectroscopic (FT-IR, FT-Raman) investigations, quantum chemical calculations, ADMET and molecular docking studies of phloretin with B-RAF inhibitor. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01576-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Kaddouri Y, Abrigach F, Ouahhoud S, Benabbes R, El Kodadi M, Alsalme A, Al-Zaqri N, Warad I, Touzani R. Synthesis, characterization, reaction mechanism prediction and biological study of mono, bis and tetrakis pyrazole derivatives against Fusarium oxysporum f. sp. Albedinis with conceptual DFT and ligand-protein docking studies. Bioorg Chem 2021; 110:104696. [PMID: 33652343 DOI: 10.1016/j.bioorg.2021.104696] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 12/18/2020] [Accepted: 01/28/2021] [Indexed: 11/20/2022]
Abstract
Twelve heterocyclic compounds were prepared using the condensation of hydroxymethanol pyrazole derivatives with different primary aminesas example 2-aminothiazole and 1-aminobenzotriazole to have a diverse productin good yield up to 97%. Those ligands were tested against Fusarium oxysporum f. sp. Albedinis fungi (BAYOUD Disease) with IC50 = 25.6-33.2 µg/ml. After experiments, theoretical investigations were done as DFT study to know the ligands molecular reactivity and the-ligandprotein- docking study to know the possible binding between the prepared ligands with two biological targets: FGB1 (Fusarium oxysporum Guanine nucleotide-binding protein beta subunitprimary amino acid sequence) and Fophy (Fusarium oxysporum phytase domain enzyme). Of all the obtained results, the experimental ones were well correlated with the theoretical with the most common thing between those compounds is (Nδ--Nδ+) which is the antifungal pharmacophore as proposed pincers for Foa inhibition. From docking studies over FGB1 and Fophy, the ligand 9 has the best binding energy of -6.4872 kcal/mol in FGB1 active site and -5.5282 kcal/mol in Fophy active site, but better correlation with Fophy than FGB1 which is followed by PLIF graph to get that Arg116, Arg120 and Lys336 are the vital amino acids of fophy protein based the study over the chosen active site.
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Affiliation(s)
- Yassine Kaddouri
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco.
| | - Farid Abrigach
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco
| | - Sabir Ouahhoud
- Laboratory of Biochemistry (LB), Department of Biology, Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Redouane Benabbes
- Laboratory of Biochemistry (LB), Department of Biology, Faculty of Sciences, University Mohamed Premier, Oujda, Morocco
| | - Mohamed El Kodadi
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco; Laboratoire d'Innovation en Sciences, Technologie et Education (LISTE), CRMEF Oriental, Oujda, Morocco
| | - Ali Alsalme
- Department of chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Nabil Al-Zaqri
- Department of chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; Department of Chemistry, College of Science, Ibb University, P. O. Box 70270, Ibb, Yemen
| | - Ismail Warad
- Department of Chemistry, Science College, An-Najah National University, PB 7, Nablus, Palestine
| | - Rachid Touzani
- Laboratory of Applied Chemistry and Environment (LCAE), Faculty of Sciences, University Mohammed Premier, Oujda, Morocco
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11
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Experimental approach, theoretical investigation and molecular docking of 2- chloro-5-fluoro phenol antibacterial compound. Heliyon 2020; 6:e05464. [PMID: 33251354 PMCID: PMC7679262 DOI: 10.1016/j.heliyon.2020.e05464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 11/22/2022] Open
Abstract
The molecular structural dimerization of biologically potent 2-chloro-5-fluoro phenol (2C5FP) is optimized. A combined experimental and theoretical characteristics of vibrational spectral determinations (NMR, FT-IR and Raman) on 2-chloro-5-fluoro phenol (2C5FP) were used at DFT-B3LYP/6–31++G (d,p) level of computation. A close coherence is achieved when experimentally observed wave numbers are compared with calculated wave numbers by refinement of the scale factors. Calculated values of global chemical descriptors of the present molecule reveal significant molecular stability and chemical reactivity. Non-Linear optical (NLO) property of the present molecule is investigated by determining the second order non linear parameter of first hyperpolarizability β. Moreover, hydrogen bond and thermodynamic parameters at various temperatures are determined and discussed. Investigated compound 2C5FP possesses a better antibacterial activity against Echerichia coli, Streptococcus aureus, Pseudomonas aureus,and Staphylococcus aureus, respectively. The title molecule is subjected to molecular docking studies with two different proteins, namely Staphylococcus aureus Tyrosyl-tRNA synthetase (PDB ID: 1JIL) and human dihydroorotate dehydrogenase (hDHODH) (PDB ID: 6CJF). The results of molecular docking analysis support the antibacterial activity and demonstrate a strong interaction with the DHODH inhibitor.
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Rahuman MH, Muthu S, Raajaraman BR, Raja M, Umamahesvari H. Investigations on 2-(4-Cyanophenylamino) acetic acid by FT-IR,FT-Raman, NMR and UV-Vis spectroscopy, DFT (NBO, HOMO-LUMO, MEP and Fukui function) and molecular docking studies. Heliyon 2020; 6:e04976. [PMID: 33005793 PMCID: PMC7511746 DOI: 10.1016/j.heliyon.2020.e04976] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/26/2020] [Accepted: 09/16/2020] [Indexed: 01/18/2023] Open
Abstract
Extensive quantum chemical calculation have been carried out to investigate the Fourier Transform Infrared(FT-IR), Fourier Transform Raman(FT-RAMAN) and Nuclear magnetic resonance(NMR), and Ultra Violet-Visible(UV-vis) spectra of 2-(4-Cyanophenylamino) acetic acid. The molecular structure, fundamental vibrational frequencies and intensities of the vibrational bands were interpreted with the aid of optimizations and normal coordinate force field calculations based on density functional theory (DFT) and ab initio HF methods with 6–311++G(d,p) basis set. The theoretical vibrational wavenumbers are compared with the experimental values. The calculated HOMO-LUMO energies were found to be-6.2056 eV and -1.2901 eV which indicates the charge transfer within the molecule. Natural bond orbital analysis has been carried out to explain the charge transfer (or) delocalization of charge due to the intra molecular interactions. Molecular Electrostatic Potential (MEP), First order hyperpolarizability, and Fukui functions calculation were also performed. The thermodynamic properties of the title compound were studied for different temperatures. Molecular docking studies were made on the title compound to study the hydrogen bond interactions and the minimum binding energy was calculated.
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Affiliation(s)
- M Habib Rahuman
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604 407, Tamil Nadu, India
| | - S Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604 407, Tamil Nadu, India.,Department of Physics, PuratchiThalaivar Dr. MGR Govt Arts and Science College, Uthiramerur, 603 406, Tamil Nadu, India
| | - B R Raajaraman
- Department of Physics, St. Joseph College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
| | - M Raja
- Department of Physics, Government Thirumagal Mills College, Vellore 635 803, Tamil Nadu, India
| | - H Umamahesvari
- Department of Science and Humanities, Sreenivasa Institute of Technology and Management Studies (Autonomous), Chittoor 517127, Andhra Pradesh, India
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13
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Ribaudo G, Bortoli M, Pavan C, Zagotto G, Orian L. Antioxidant Potential of Psychotropic Drugs: From Clinical Evidence to In Vitro and In Vivo Assessment and toward a New Challenge for in Silico Molecular Design. Antioxidants (Basel) 2020; 9:E714. [PMID: 32781750 PMCID: PMC7465375 DOI: 10.3390/antiox9080714] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
Due to high oxygen consumption, the brain is particularly vulnerable to oxidative stress, which is considered an important element in the etiopathogenesis of several mental disorders, including schizophrenia, depression and dependencies. Despite the fact that it is not established yet whether oxidative stress is a cause or a consequence of clinic manifestations, the intake of antioxidant supplements in combination with the psychotropic therapy constitutes a valuable solution in patients' treatment. Anyway, some drugs possess antioxidant capacity themselves and this aspect is discussed in this review, focusing on antipsychotics and antidepressants. In the context of a collection of clinical observations, in vitro and in vivo results are critically reported, often highlighting controversial aspects. Finally, a new challenge is discussed, i.e., the possibility of assessing in silico the antioxidant potential of these drugs, exploiting computational chemistry methodologies and machine learning. Despite the physiological environment being incredibly complex and the detection of meaningful oxidative stress biomarkers being all but an easy task, a rigorous and systematic analysis of the structural and reactivity properties of antioxidant drugs seems to be a promising route to better interpret therapeutic outcomes and provide elements for the rational design of novel drugs.
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Affiliation(s)
- Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy;
| | - Marco Bortoli
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy;
| | - Chiara Pavan
- Dipartimento di Medicina, Università degli Studi di Padova, Via Giustiniani 2, 35128 Padova, Italy;
| | - Giuseppe Zagotto
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via Marzolo 5, 35131 Padova, Italy;
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy;
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14
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Lu L, Luo K, Yang W, Zhang S, Wang W, Xu H, Wu S. Insight into the anti-aging mechanisms of natural phenolic antioxidants in natural rubber composites using a screening strategy based on molecular simulation. RSC Adv 2020; 10:21318-21327. [PMID: 35518775 PMCID: PMC9054403 DOI: 10.1039/d0ra03425h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/19/2020] [Indexed: 12/05/2022] Open
Abstract
The failure of materials upon aging has led to the accumulation of waste and environmental pollution. Adding antioxidants (AOs) to the composites is one of the most effective ways to retard aging. However, traditional synthetic AOs are always detrimental to the environment and human health. The selection of antioxidants from streams by experiments will also definitely cost a lot of time and money. In addition, the complexity of thermo-oxidative aging factors along with the lack of quantitative tools significantly hampers its applications. So, building a screening strategy to quickly and easily find an appropriate and eco-friendly AO is imperative. In this study, we chose natural rubber (NR) as a matrix and provided a screening strategy based on diverse natural phenolic antioxidants to evaluate their ability in protecting NR composites. Thymol, α-tocopherol, and lipid-soluble epigallocatechin gallate (lsEGCG) were chosen from 18 natural phenolic antioxidants as potential alternative candidates. They were proved, indeed, to enhance the oxidative time in NR from experiments. Our results emphasized that thymol, α-tocopherol, and lsEGCG were promising alternatives for AOs in NR, and the in vitro toxicity test suggested that they are biocompatible. This study may develop a new strategy preference for screening the antioxidants by combining molecular simulation with the validation of experimental approaches, and therefore guide the AO molecular design with a more accurate theoretical prediction.
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Affiliation(s)
- Ling Lu
- State Key Laboratory of Organic-Inorganic composites, Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Kaiqiang Luo
- State Key Laboratory of Organic-Inorganic composites, Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Wei Yang
- Global Energy Interconnection Research Institute, State Key Laboratory of Advanced Power Transmission Technology Beijing 102211 P. R. China
| | - Sidian Zhang
- State Key Laboratory of Organic-Inorganic composites, Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Wencai Wang
- State Key Laboratory of Organic-Inorganic composites, Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Haiyan Xu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College Beijing 100005 P. R. China
| | - Sizhu Wu
- State Key Laboratory of Organic-Inorganic composites, Beijing University of Chemical Technology Beijing 100029 P. R. China
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15
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Haruna K, Kumar VS, Armaković SJ, Armaković S, Mary YS, Thomas R, Popoola SA, Almohammedi AR, Roxy MS, Al-Saadi AA. Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117580. [PMID: 31748158 DOI: 10.1016/j.saa.2019.117580] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/16/2019] [Accepted: 09/28/2019] [Indexed: 06/10/2023]
Abstract
A set of experimental and computational techniques have been applied for the understanding of fundamental spectroscopic and reactive properties of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) compound. Experimental techniques employed in this study encompassed spectroscopic characterization via IR and Raman approaches, while optical properties were studied by measurements of UV/Vis spectra. The thermogravimetric analysis was also studied in order to analyze the stability of diuron. Aside from the determination of reactive properties, DFT calculations on isolated molecules were also used to thoroughly visualize and analyze spectroscopic properties such as IR and UV/Vis. MD simulations were used in order to understand interactions with water, while periodic DFT calculations were used in order to analyze band structure and density of states of the diuron crystal structure. Since the crystal structure of diuron is known, it was used in order to extract the relevant molecular pairs and investigate interactions between them by DFT and symmetry adapted perturbation theory approaches (SAPT).
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Affiliation(s)
- K Haruna
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Veena S Kumar
- Department of Physics, SN College, Kollam, Kerala, India; Research Centre, University of Kerala, Kerala, India
| | - Sanja J Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000, Novi Sad, Serbia
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000, Novi Sad, Serbia
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, 686101, Kerala, India.
| | - Saheed A Popoola
- Department of Chemistry, Islamic University of Madinah, Saudi Arabia
| | - A R Almohammedi
- Department of Physics, Islamic University of Madinah, Saudi Arabia
| | - M S Roxy
- Department of Physics, SN College, Kollam, Kerala, India
| | - A A Al-Saadi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
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16
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Saji RS, Prasana JC, Muthu S, George J, Kuruvilla TK, Raajaraman BR. Spectroscopic and quantum computational study on naproxen sodium. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117614. [PMID: 31606674 DOI: 10.1016/j.saa.2019.117614] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/05/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
The spectroscopic (FT-IR, FT-Raman, NMR), electronic (UV--Vis.), structural and thermodynamical properties of an anti-inflammatory analgesic called Naproxen Sodium, (s)-6-methoxy-α-methyl-2-naphthaleneacetic acid sodium salt are submitted by using both experimental techniques and theoretical methods as quantum chemical calculations in this work. The equilibrium geometry and vibrational spectra are calculated by using DFT (B3LYP) with 6-311++G (d,p) basis set using GAUSSIAN 09. The vibrational wavenumbers are also corrected with scale factor to take better results for the calculated data. The HOMO-LUMO calculations are carried out on the title compound. The theoretical and experimental NMR peaks were found to be in good agreement. In addition, the detailed study on the Non-Bonding Orbitals, the excitation energies, AIM charges, condensed fukui calculations, thermodynamical properties, Localized Orbital Locator (LOL) and Electron Localization Function (ELF) are also performed. Furthermore, the study is extended to calculate the first order hyperpolarizability and to predict its NLO properties. The docking studies details helped on predicting the binding with different proteins.
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Affiliation(s)
- Rinnu Sara Saji
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India; University of Madras, Chennai, 600005, Tamilnadu, India
| | | | - S Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, 604407, Tamil Nadu, India.
| | - Jacob George
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India
| | - Tintu K Kuruvilla
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India
| | - B R Raajaraman
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
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17
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Al-Otaibi JS, Mary YS, Armaković S, Thomas R. Hybrid and bioactive cocrystals of pyrazinamide with hydroxybenzoic acids: Detailed study of structure, spectroscopic characteristics, other potential applications and noncovalent interactions using SAPT. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127316] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Ben Geoffrey AS, Prasana JC, Muthu S, Abraham CS, David HA. Structure–Activity relationship studies of two dietary flavonoids and their Nitric Oxide Synthase inhibition activity by spectroscopic and quantum/classical computational techniques. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Nitric Oxide Synthase inhibitory activity of two dietary phytocompounds naringenin and quercetin that belong to the family of flavonoids was studied by spectroscopic and computational methods. The determining role played by the global reactivity parameters that were calculated using spectroscopic and computational methods were correlated with the Nitric Oxide Synthase inhibitory activity by a Quantitative Structure–Activity Relationship (QSAR) study. The inter and intramolecular charge–transfer interactions responsible for the biological activity of naringenin and quercetin were studied using Natural Bond Orbital Analysis. The reactive sites of the title compounds were studied using their molecular electrostatic map. The likelihood of naringenin and quercetin to be a small drug molecule was determined by Lipinski’s rule. The molecular dynamics and docking studies were carried out to test the energetic and structural favorability of the inhibition of Nitric Oxide Synthase by small drug molecules naringenin and quercetin. Experimental cell culture-based in vitro assays were done to test theoretical predictions. A QSAR study revealed that for Nitric Oxide Synthase inhibitory activity to be better, the compounds belonging to the family of flavonoids ought to have a more negative ionization energy and chemical softness while bandgap and electrophilicity index ought to be more positive.
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Affiliation(s)
- A. S. Ben Geoffrey
- Department of Physics, Madras Christian College, East Tambaram 600059, Tamil Nadu, India
- University of Madras, Chepauk, Chennai-005, Tamil Nadu, India
| | - Johanan Christian Prasana
- Department of Physics, Madras Christian College, East Tambaram 600059, Tamil Nadu, India
- University of Madras, Chepauk, Chennai-005, Tamil Nadu, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar 604407, Tamil Nadu, India
| | - Christina Susan Abraham
- Department of Physics, Madras Christian College, East Tambaram 600059, Tamil Nadu, India
- University of Madras, Chepauk, Chennai-005, Tamil Nadu, India
| | - Host Antony David
- Entomological Research Centre, Loyola College, Chennai, Tamil Nadu-600034, India
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19
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A S BG, Prasana JC, Muthu S, Abraham CS, David HA. Spectroscopic and quantum/classical mechanics based computational studies to compare the ability of Andrographolide and its derivative to inhibit Nitric Oxide Synthase. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 218:374-387. [PMID: 31030004 DOI: 10.1016/j.saa.2019.04.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
The inhibition of the enzyme Nitric Oxide Synthase by a bioactive compounds results in it possessing anti-inflammatory property. The ability of Andrographolide and its derivative Isoandrographolide to inhibit Nitric Oxide Synthase was studied using computational and experimental techniques. A combination of UV Spectroscopic and DFT computational techniques were used to calculate the molecular descriptors of the title compounds which were used to establish relationship with its biological activity. The drug-likeness of the compounds was estimated using Lipinski's rule. Molecular dynamics and docking studies were carried out to test for the structural and energetic favourability of the title compounds(ligand) being bound to Nitric Oxide Synthase(Protein) to induce inhibition. The force constant data obtained from IR spectroscopy was used in aid to parametrize force fields used in molecular dynamics simulation. The DFT method was used to perform NBO analysis that revealed the charge transfer interactions responsible for its biological properties. The Molecular Electrostatic Potential (MEP) plot revealed the regions of electrophilic and nucleophilic reactivity of the title compounds. MTT (3-(4, 5-dimethyl thiazolyl-2)-2, 5-diphenyltetrazolium bromide) assay was carried out which revealed the cytotoxicity at different concentrations of the title compounds by which means the biologically safe concentration was determined and therefore at this biologically safe concentration the ability of the compounds to inhibit Nitric Oxide formation was determined. Quantitative Structure-Activity Studies (QSAR) were used to furnish relationship between molecular descriptors and the Nitric Oxide Synthase inhibition activity resulting in anti-inflammatory property, based on the chosen molecular descriptors suggestions were made for the search of more potent Nitric Oxide Synthase inhibitors in the Andrographolide derivative family of compounds.
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Affiliation(s)
- Ben Geoffrey A S
- Department of Physics, Madras Christian College, East Tambaram 600059, Tamil Nadu, India
| | | | - S Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar 604407, Tamil Nadu, India.
| | | | - Host Antony David
- Bioinformatics Centre of BTISnet, Madras Christian College, Chennai, Tamil Nadu 600059, India
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20
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Raajaraman BR, Sheela NR, Muthu S. Spectroscopic, quantum computational and molecular docking studies on 1-phenylcyclopentane carboxylic acid. Comput Biol Chem 2019; 82:44-56. [PMID: 31260880 DOI: 10.1016/j.compbiolchem.2019.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/18/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022]
Abstract
The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Using potential energy distribution, all the assignments of the basic vibrational modes were calculated. Natural bond orbital (NBO) and atoms in molecules (AIM) topological studies applied to get the intermolecular interactions of the compound. 1H and 13C chemical shift of NMR was estimated on the molecule and also compared with the experimental spectra. In order to find the band gap, the time-dependent (TD-DFT) method is used to get the higher order energy levels properties and also compared with experimental data of UV-vis spectrum. From the analysis of various spectroscopic studies, there is a good relationship between the experimental and theoretical values obtained. Quantum characters, bio-active nature and reactive areas of the molecule are revealed by Fukui function, molecular electrostatic potential (MEP) and Hirshfeld surface studies. The human enzyme steroidogenic types and their protein targets were tested with this molecule by molecular docking.
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Affiliation(s)
- B R Raajaraman
- Department of Applied Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
| | - N R Sheela
- Department of Applied Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
| | - S Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604 407, Tamil Nadu, India.
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