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R S, Mahalakshmi S, Kumaran S, Kadaikunnan S, Abbas G, Muthu S. Structural, electronic, intermolecular interaction, reactivity, vibrational spectroscopy, charge transfer, Hirshfeld surface analysis, pharmacological and hydropathy plot on 5-Bromo nicotinic acid - Antiviral study (Hepatitis A, B, and C). Heliyon 2023; 9:e19965. [PMID: 37809934 PMCID: PMC10559560 DOI: 10.1016/j.heliyon.2023.e19965] [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: 07/28/2023] [Revised: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
The therapeutic properties of 5-Bromonicotinatic acid (5BNA) were studied for antiviral illnesses like Hepatitis A, Hepatitis B and Hepatitis C and the influence of electron-donating and electron-withdrawing properties of functional groups on the nicotinic acid was evaluated and represented in this study using the DFT approach. The molecular parameters were determined for both gases as well as for various solvent phases. The reactive areas in the compound are examined utilising Fukui analysis. The molecular interactions are accomplished by recognising the different types of bonding found in the compound using the AIM, ELF, LOL, RDG and IRI. Solvation investigations were demonstrated to have an influence on molecular orbital energy, ESP, UV-Vis and NLO analyses. Electron-hole, NBO and Hirshfeld investigations are used to investigate the transfer of charges and interactions inside the molecule. The method of vibrational spectroscopy (IR and Raman) is used to differentiate and identify the various types of vibrations displayed by the compound. The hydropathy plots for the proteins 2A4O, 6CWD and 2OC8 associated with Hepatitis A, Hepatitis B and Hepatitis C illustrate the disquiet and attraction of the amino acids towards the water.
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Affiliation(s)
- Sravanthi R
- Department of Physics, Ethiraj College for Women, Chennai, 600008, Tamil Nadu, India
- University of Madras, Chennai, 600005, Tamil Nadu, India
| | - S. Mahalakshmi
- Department of Physics, Ethiraj College for Women, Chennai, 600008, Tamil Nadu, India
| | - S. Kumaran
- Department of ECE, Saveetha Engineering College, Thandalam, Chennai, 602105, Tamil Nadu, India
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ghulam Abbas
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology, Engesserstr 15, 76131, Karlsruhe, Germany
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604407, Tamil Nadu, India
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R S, Mahalakshmi S, Vetrivelan V, Irfan A, Muthu S. Absorption wavelength (TD-DFT) and adsorption of metal chalcogen clusters with methyl nicotinate: Structural, electronic, IRI, SERS, pharmacological and antiviral studies (HIV and omicron). Heliyon 2023; 9:e16066. [PMID: 37234664 PMCID: PMC10208831 DOI: 10.1016/j.heliyon.2023.e16066] [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: 02/27/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The DFT B3LYP-LAND2DZ technique is used to examine interactions of Methyl nicotinate with copper selenide and zinc selenide clusters. The existence of reactive sites is determined using ESP maps and Fukui data. The energy variations between HOMO and LUMO are utilised to calculate various energy parameters. The Atoms in Molecules and ELF (Electron Localisation Function) maps are employed to investigate the topology of the molecule. The Interaction Region Indicator is used to determine the existence of non-covalent zones in the molecule. The UV-Vis spectrum using the TD-DFT method and DOS graphs are used to obtain the theoretical determination of electronic transition and properties. Structural analysis of the compound is obtained using theoretical IR spectra. To explore the adsorption of copper selenide and zinc selenide clusters on the Methyl nicotinate, the adsorption energy and theoretical SERS spectra are employed. Furthermore, pharmacological investigations are carried out to confirm the drug's non-toxicity. The compound's antiviral efficacy against HIV and Omicron is demonstrated via protein-ligand docking.
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Affiliation(s)
- Sravanthi R
- Department of Physics, Ethiraj College for Women, Chennai, 600008, Tamil Nadu, India
- University of Madras, Chennai, 600005, Tamil Nadu, India
| | - S. Mahalakshmi
- Department of Physics, Ethiraj College for Women, Chennai, 600008, Tamil Nadu, India
| | - V. Vetrivelan
- Department of Physics, Government College of Engineering, Srirangam, Trichy 620012, Tamil Nadu, India
| | - Ahmad Irfan
- Department of Chemistry, College of Science, King Khalid University, P. O. Box 9004, Abha, 61413, Saudi Arabia
| | - S. Muthu
- Department of Physics, Arignar Anna Govt.Arts College, Cheyyar, 604407, Tamil Nadu, India
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Synthesis, crystal structure, Hirshfeld surface, energy framework, NCI-RDG, theoretical calculations and molecular docking of (Z)4,4′-bis[-3-N-ethyl-2-N'-(phenylimino) thiazolidin-4-one] methane. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nekrouf A, Toubal K, Megrouss Y, Belkafouf NEH, Djafri A, Khelloul N, Daran JC, Djafri A, Chouaih A. Synthesis, structural, spectroscopic, intermolecular interactions, kinetic stability, charge transfer method with DNA bases and electronic properties of (E)-3-(2-ethoxyphenyl)-5-(3-(2-methoxyphenyl)-4methylthiazol-2(3H)-ylidene)-2-thioxothiazolidin-4-one: Computational and experimental approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Rahmani R, Perveen F, Benhalima N, Djafri A, Khelloul N, Chouaih A, Djafri A, Kanoun MB, Goumri-Said S. FTIR, NMR and UV–Visible Spectral Investigations, Theoretical Calculations, Topological Analysis, Chemical Stablity, and Molecular Docking Study on Novel Bioactive Compound: The 5-(5-Nitro Furan-2-Ylmethylen), 3- N-(2-Methoxy Phenyl),2- N′- (2-Methoxyphenyl) Imino Thiazolidin-4-One. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2094971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Rachida Rahmani
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University - Mostaganem, Mostaganem, Algeria
- Department of Process Engineering, Faculty of Sciences and Technology, Ahmed Zabana - University of Relizane, Relizane, Algeria
| | - Fouzia Perveen
- Research Centre for Modeling and Simulation, National University of Science and Technology, Islamabad, Pakistan
| | - Nadia Benhalima
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University - Mostaganem, Mostaganem, Algeria
- Physics Department, Faculty of Sciences, Dr. Tahar Moulay University of Saida, Saida, Algeria
| | - Ahmed Djafri
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University - Mostaganem, Mostaganem, Algeria
- Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques (CRAPC), Tipaza, Algeria
| | - Nawel Khelloul
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University - Mostaganem, Mostaganem, Algeria
- Faculty of Sciences and Technology, Mustapha Stambouli University of Mascara, Mascara , Algeria
| | - Abdelkader Chouaih
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University - Mostaganem, Mostaganem, Algeria
| | - Ayada Djafri
- Laboratoire de Synthèse Organique Appliquée (LSOA), Département de Chimie, Faculté Des Sciences, Université D'Oran 1 - Ahmed Ben Bella, Oran, Algeria
| | - Mohammed Benali Kanoun
- Department of Physics, College of Science, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Souraya Goumri-Said
- College of Science, Department of Physics, Alfaisal University, Riyadh, Saudi Arabia
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Saidj M, Djafri A, Rahmani R, Belkafouf NEH, Boukabcha N, Djafri A, Chouaih A. Molecular Structure, Experimental and Theoretical Vibrational Spectroscopy, (HOMO-LUMO, NBO) Investigation, (RDG, AIM) Analysis, (MEP, NLO) Study and Molecular Docking of Ethyl-2-{[4-Ethyl-5-(Quinolin-8-yloxyMethyl)-4H-1,2,4-Triazol-3-yl] Sulfanyl} Acetate. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2039238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Merzouk Saidj
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
| | - Ahmed Djafri
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
- Organic Synthesis Division, Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques (CRAPC), Tipaza, Algérie
| | - Rachida Rahmani
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
- Department of Process Engineering, Faculty of Sciences and Technology, Ahmed Zabana University of Relizane, Relizane, Algeria
| | - Nour El Houda Belkafouf
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
| | - Nourdine Boukabcha
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
- Chemistry Department, Faculty of Exact Sciences and Informatic, Hassiba Benbouali University, Chlef, Algeria
| | - Ayada Djafri
- Laboratoire de Synthèse Organique Appliquées (LSOA), Faculté Des Sciences Exactes et Appliquées, Département de Chimie, Université Oran-1, Algérie
| | - Abdelkader Chouaih
- Process Engineering Department, Laboratory of Technology and Solid Properties, Faculty of Sciences and Technology, Abdelhamid Ibn Badis University, Mostaganem, Algeria
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Manimozhi PK, Kavitha R, Thilagavathi R, Gokilavani GM. Theoretical, Experimental Studies on Molecular Structure and Vibrational Spectra of 2,6-Dibromo-4-Nitrophenol. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2039228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- P. K. Manimozhi
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - R. Kavitha
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - R. Thilagavathi
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - G. M. Gokilavani
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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Linani A, Benarous K, Bou-Salah L, Yousfi M, Goumri-Said S. Exploring Structural Mechanism of COVID-19 Treatment with Glutathione as a Potential Peptide Inhibitor to the Main Protease: Molecular Dynamics Simulation and MM/PBSA Free Energy Calculations Study. Int J Pept Res Ther 2022; 28:55. [PMID: 35079241 PMCID: PMC8777181 DOI: 10.1007/s10989-022-10365-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2022] [Indexed: 01/08/2023]
Abstract
The 2019-novel coronavirus has unfolded everywhere in the world and obliged a billion human beings in open confinement, whereas many treatments, and vaccines have been proposed towards this pandemic. The main protease (Mpro) is an attractive drug target due to the fact that it is the essential protein for virus invasion. This research tests in silico the effect of five vitamins towards Mpro, by employing molecular docking (MD), molecular dynamics simulation (MDS) with molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) studies. To achieve this work, we have applied some software’s as Autodock Vina, Discovery Studio Visualizer, APBS, and GROMACS. The inhibitors used were decided entirely on the basis of their importance in the production of red blood cells that prevent anemia, in lymphocyte immune system responses, in the regulation of reactive oxygen species production, such as tocopherol (vitamin E), thiamine (vitamin B1), pantothenic acid (vitamin B5), pyridoxine (vitamin B6), biotin (vitamin B7), and glutathione (GSH). The best inhibitor pose established at the highest repetition ratio (RR) and the minimal affinity energy value (MEV), then the best selected inhibitor was considered to MDS. The results indicate that GSH is the leading inhibitor model among the other tested vitamins in the active site of Mpro with a RR value of 94% and MEV of − 5.5 kcal/mol, its RMSD, RMSF, Rg, and hydrogen bonds show stability with Mpro. Furthermore, thiamine, biotin, and tocopherol are viewed as satisfying inhibitors to Mpro, but pyridoxine was observed as the weakest inhibitor. Based on our result, we could recommend the usage of glutathione and vitamin B family as a supportive strategy for feasible remedy of COVID-19 virus.
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Affiliation(s)
- Abderahmane Linani
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Khedidja Benarous
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Leila Bou-Salah
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Mohamed Yousfi
- Fundamental Sciences Laboratory, Amar Telidji University, Laghouat, Algeria
| | - Souraya Goumri-Said
- Physics Department, College of Science, Alfaisal University, P.O. Box 50927, Riyadh, 11533 Saudi Arabia
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Mohamed Abdelahi MM, El Bakri Y, Lai CH, Subramani K, Anouar EH, Ahmad S, Benchidmi M, Mague JT, Popović-Djordjević J, Goumri-Said S. Novel 3-chloro-6-nitro-1 H-indazole derivatives as promising antileishmanial candidates: synthesis, biological activity, and molecular modelling studies. J Enzyme Inhib Med Chem 2021; 37:151-167. [PMID: 34894940 PMCID: PMC8667887 DOI: 10.1080/14756366.2021.1995380] [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] [Indexed: 11/03/2022] Open
Abstract
An efficient pathway was disclosed for the synthesis of 3-chloro-6-nitro-1H-indazole derivatives by 1,3-dipolar cycloaddition on dipolarophile compounds 2 and 3. Faced the problem of separation of two regioisomers, a click chemistry method has allowed us to obtain regioisomers of triazole-1,4 with good yields from 82 to 90% were employed. Also, the antileishmanial biological potency of the compounds was achieved using an MTT assay that reported compound 13 as a promising growth inhibitor of Leishmania major. Molecular docking demonstrated highly stable binding with the Leishmania trypanothione reductase enzyme and produced a network of hydrophobic and hydrophilic interactions. Molecular dynamics simulations were performed for TryR-13 complex to understand its structural and intermolecular affinity stability in a biological environment. The studied complex remained in good equilibrium with a structure deviation of ∼1-3 Å. MM/GBSA binding free energies illustrated the high stability of TryR-13 complex. The studied compounds are promising leads for structural optimisation to enhance the antileishmanial activity.
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Affiliation(s)
- Mohamed Mokhtar Mohamed Abdelahi
- Laboratoire de Chimie Organique Hétérocyclique, Centre de Recherche des Sciences des Médicaments, Pôle de Compétences Pharmacochimie, URAC 21, Faculté des Sciences, Mohammed V University Rabat, Rabat, Morocco
| | - Youness El Bakri
- Laboratoire de Chimie Organique Hétérocyclique, Centre de Recherche des Sciences des Médicaments, Pôle de Compétences Pharmacochimie, URAC 21, Faculté des Sciences, Mohammed V University Rabat, Rabat, Morocco.,Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
| | - Chin-Hung Lai
- Department of Medical Applied Chemistry, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Education, Chung Shan Medical University Hospital, Taichung, Taiwan
| | | | - El Hassane Anouar
- Department of Chemistry, College of Sciences and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mohammed Benchidmi
- Laboratoire de Chimie Organique Hétérocyclique, Centre de Recherche des Sciences des Médicaments, Pôle de Compétences Pharmacochimie, URAC 21, Faculté des Sciences, Mohammed V University Rabat, Rabat, Morocco
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Jelena Popović-Djordjević
- Department for Chemistry and Biochemistry, Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Souraya Goumri-Said
- College of Science, Physics Department, Alfaisal University, Riyadh, Saudi Arabia
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