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Agarwal N, Fatima A, Bhattacharya P, Muthu S, Arora H, Siddiqui N, Javed S. Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine. J Biomol Struct Dyn 2023; 41:10430-10449. [PMID: 36562198 DOI: 10.1080/07391102.2022.2159530] [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: 04/03/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Agarwal
- Department of chemistry, Institute of H. Science, Dr. Bhimrao-Ambedkar University, Agra, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | | | - S Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, India
| | - Himanshu Arora
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
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Tchaikovskaya O, Bocharnikova E, Bazyl O, Chaidonova V, Mayer G, Avramov P. Nature of Luminescence and Pharmacological Activity of Sulfaguanidine. Molecules 2023; 28:molecules28104159. [PMID: 37241901 DOI: 10.3390/molecules28104159] [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: 04/18/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Sulfonamides are one of the oldest groups of veterinary chemotherapeutic agents. Physico-chemical properties, the concentration and the nature of the environment are the factors responsible for the distribution of sulfonamides in the living organism. Although these drug compounds have been in use for more than half a century, knowledge about their behavior is still limited. Physiological activity is currently attributed to the sulfanyl radical. Our study is devoted to the spectral properties of aqueous solutions of sulfaguanidine, in which the formation of complexes with an H-bond and a protonated form takes place. The nature of the fluorescent state of sulfaguanidine was interpreted using computational chemistry, the electronic absorption method and the luminescence method. The structure of sulfaguanidine includes several active fragments: aniline, sulfonic and guanidine. To reveal the role of fragments in the physiological activity of the studied antibiotic, we calculated and compared the effective charges of the fragments of aniline and sulfaguanidine molecules. Chromophore groups were identified in molecules, which determine the intermolecular interaction between a molecule and a proton-donor solvent. The study also revealed the impact of sulfone and guanidine groups, as well as complexation, on the effective charge of the antibiotic fragment responsible for physiological activity and luminescent ability.
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Affiliation(s)
- Olga Tchaikovskaya
- Quantum Electronics Laboratory, Institute of Electrophysics, Ural Branch of the Russian Academy of Sciences, 620146 Yekaterinburg, Russia
- Laboratory of Photophysics and Photochemistry of Molecules, Faculty of Physics, Tomsk State University, 634050 Tomsk, Russia
| | - Elena Bocharnikova
- Laboratory of Photophysics and Photochemistry of Molecules, Faculty of Physics, Tomsk State University, 634050 Tomsk, Russia
| | - Olga Bazyl
- Laboratory of Photophysics and Photochemistry of Molecules, Faculty of Physics, Tomsk State University, 634050 Tomsk, Russia
| | - Vlada Chaidonova
- Laboratory of Photophysics and Photochemistry of Molecules, Faculty of Physics, Tomsk State University, 634050 Tomsk, Russia
- Hygienic and Epidemiological Center in Republic of Khakassia, 655017 Abakan, Russia
| | - George Mayer
- Laboratory of Photophysics and Photochemistry of Molecules, Faculty of Physics, Tomsk State University, 634050 Tomsk, Russia
| | - Paul Avramov
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
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Fatima A, Ali A, Rajan R, Verma I, Muthu S, Siddiqui N, Garg P, Javed S. Experimental Spectroscopic, DFT, Molecular Docking, and Molecular Dynamics Simulation Investigations on m-Phenylenediamine (Monomer and Trimer). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2150655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, India
| | - Akram Ali
- Department of Chemistry, CMP College, Allahabad, India
| | - Ramya Rajan
- Department of Chemistry, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | - S. Muthu
- Department of Physics, Aringnar Anna Govt. Arts College, Cheyyar, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, India
| | - Pankaj Garg
- Department of Chemistry, GLA University, Mathura, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, India
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Manhas FM, Fatima A, Verma I, Siddiqui N, Muthu S, AlSalem HS, Savita S, Singh M, Javed S. Quantum computational, spectroscopic (FT-IR, NMR and UV–Vis) profiling, Hirshfeld surface, molecular docking and dynamics simulation studies on pyridine-2,6-dicarbonyl dichloride. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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DFT, Molecular Docking, Molecular Dynamics Simulation (MMGBSA) and Hirshfeld Surface Analysis of 5-Sulfosalicylic Acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134242] [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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Sharma S, Fatima A, Manhas FM, Agarwal N, Singh M, Muthu S, Siddiqui N, Javed S. Experimental Spectroscopic, Quantum Chemical, Molecular Docking, and Molecular Dynamic Simulation Studies on Hydantoin (Monomer and Dimer). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2123540] [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)
- Shikha Sharma
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Farah Manzer Manhas
- Department of Chemistry, Shoolini University, Solan, Himachal Pradesh, India
| | - Neha Agarwal
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Meenakshi Singh
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - S. Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, Tamil Nadu, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
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Sepay N, Chakrabarti S, Afzal M, Alarifi A, Mal D. Identification of 4-acrylamido- N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study. RSC Adv 2022; 12:24178-24186. [PMID: 36128538 PMCID: PMC9403657 DOI: 10.1039/d2ra04333e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022] Open
Abstract
Omicron is one of the variants of COVID-19 and continuing member of a pandemic. There are several types of vaccines that were developed around the globe to fight against the virus. However, the world is suffering to find suitable drug candidates for the virus. The main protease (Mpro) enzyme of the virus is the best target for finding drug molecules because of its involvement in viral infection and protein synthesis. ZINC-15 is a database of 750 million commercially available compounds. We find 125 compounds having two aromatic rings and amide groups for non-covalent interactions with active site amino acids and functional groups with the capability to bind -SH group of C145 of Mpro through covalent bonding by a nucleophilic addition reaction. The lead compound (Z144) was identified using molecular docking. The non-covalent interactions (NCI) calculations show the interactions between amino acids present in the active site of the protein and the lead molecules are attractive in nature. The density functional-based tight-binding (DFTB) study of the lead compound with amino acids in the active site indicates that Q190 and Q193 play a very critical role in stabilization. The Michael addition of the acrylamide group of the lead molecule at β-position is facile because the low energy lowest unoccupied molecular orbital (LUMO) is concentrated on the group. From molecular dynamics during 100 ns, it has come to light that strong non-covalent interactions are key for the stability of the lead inside the protein and such binding can fold the protein. The free energy for this interaction is -42.72 kcal mol-1 which was obtained from MM-GB/SA calculations.
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Lady Brabourne College Kolkata 700017 India
| | | | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Dasarath Mal
- Department of Chemistry, Vijaygarh Jyotish Ray College Kolkata 700032 India
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Fatima A, Khanum G, Sharma A, Siddiqui N, Muthu S, Butcher R, Srivastava SK, Javed S. Synthesis, Single crystal X-ray, DFT, Hirshfeld Surface and molecular docking studies of 9-(2,4-dichlorophenyl)-4a-hydroxy-tetramethyl-octahydro-1H-xanthene-1,8(2H)-dione. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Fatima A, Khanum G, Agrawal DD, Srivastava SK, Butcher RJ, Muthu S, Ahmad M, Althubeiti K, Siddiqui N, Javed S. Synthesis, Spectroscopic, Crystal Structure, DFT, Hirshfeld Surface and Molecular Docking Analysis of Hexahydroquinoline Derivative (HQ). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2089174] [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)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhaya Pradesh, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhaya Pradesh, India
| | - Dau D. Agrawal
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhaya Pradesh, India
| | | | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, District of Columbia, USA
| | - S. Muthu
- Department of Physics, Aringnar Anna Govt. Arts College, Cheyyar, India
| | - Musheer Ahmad
- Department of Applied Chemistry, Faculty of Engineering and Technology, ZHCET, Aligarh Muslim University, Aligarh, India
| | - Khaled Althubeiti
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Dr. Bhimrao Ambedkar University, Agra, Uttar Pradesh, India
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Pooja K, Fatima A, Sharma A, Garima K, Savita S, Kumar M, Verma I, Siddiqui N, Javed S. Experimental, theoretical, hirschfeld surface, electronic excitation and molecular docking studies on fomepizole(4-Methyl-1H-pyrazole). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132549] [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]
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Kumar M, Fatima A, Singh M, Verma I, Khanum G, Muthu S, Althubeiti K, Abualnaja KM, Ahmad M, Siddiqui N, Javed S. Experimental Spectroscopic, Quantum Computational, Hirshfeld Surface, Molecular Docking, and Electronic Excitation Studies on an Antibiotic Agent: SDZ. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2063909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mukesh Kumar
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao-Amedkar University, Agra, Uttar Pradesh, India
- Department of Chemistry, Shri Khushal Das University, Hanumangarh, Rajasthan, India
| | - Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Meenakshi Singh
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao-Amedkar University, Agra, Uttar Pradesh, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, Tamil Nadu, India
| | - Khaled Althubeiti
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - khamael M. Abualnaja
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Musheer Ahmad
- Department of Applied Chemistry, Faculty of Engineering and Technology, ZHCET, Aligarh Muslim University, Aligarh, India
| | - Nazia Siddiqui
- USIC, Dayalbagh Educational Institute, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao-Amedkar University, Agra, Uttar Pradesh, India
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Singh N, Fatima A, Singh M, kumar M, Verma I, Muthu S, Siddiqui N, Javed S. Exploration of experimental, theoretical, Hirshfeld surface, molecular docking and electronic excitation studies of Menadione: A potent anti-cancer agent. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118670] [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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Rationalizing the Role of Electron/Charge Transfer in the Intramolecular Chemiexcitation of Dioxetanone-Based Chemi-/Bioluminescent Systems. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113904] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Dardeer HM, Toghan A, Zaki MEA, Elamary RB. Design, Synthesis and Evaluation of Novel Antimicrobial Polymers Based on the Inclusion of Polyethylene Glycol/TiO 2 Nanocomposites in Cyclodextrin as Drug Carriers for Sulfaguanidine. Polymers (Basel) 2022; 14:polym14020227. [PMID: 35054634 PMCID: PMC8780372 DOI: 10.3390/polym14020227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Polymers and their composites have recently attracted attention in both pharmaceutical and biomedical applications. Polyethylene glycol (PEG) is a versatile polymer extensively used in medicine. Herein, three novel PEG-based polymers that are pseudopolyrotaxane (PEG/α-CD) (1), titania–nanocomposite (PEG/TiO2NPs) (2), and pseudopolyrotaxane–titania–nanocomposite (PEG/α-CD/TiO2NPs) (3), were synthesized and characterized. The chemical structure, surface morphology, and optical properties of the newly materials were examined by FT-IR, 1H-NMR, SEM, and UV–Vis., respectively. The prepared polymers were used as drug carriers of sulfaguanidine as PEG/α-CD/Drug (4), PEG/TiO2NPs/Drug (5), and PEG/α-CD/TiO2NPs/Drug (6). The influence of these drug-carrying formulations on the physical and chemical characteristics of sulfaguanidine including pharmacokinetic response, solubility, and tissue penetration was explored. Evaluation of the antibacterial and antibiofilm effect of sulfaguanidine was tested before and after loading onto the prepared polymers against some Gram-negative and positive bacteria (E. coli, Pseudomonas aeruginosa, and Staphylococcus aureus (MRSA)), as well. The results of this work turned out to be very promising as they confirmed that loading sulfaguanidine to the newly designed polymers not only showed superior antibacterial and antibiofilm efficacy compared to the pure drug, but also modified the properties of the sulfaguanidine drug itself.
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Affiliation(s)
- Hemat M. Dardeer
- Chemistry Department, Faculty of Science, South Valley University, Qena 83523, Egypt;
| | - Arafat Toghan
- Chemistry Department, Faculty of Science, South Valley University, Qena 83523, Egypt;
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia;
- Correspondence: or
| | - Magdi E. A. Zaki
- Chemistry Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia;
| | - Rokaia B. Elamary
- Botany and Microbiology Department, Faculty of Science, South Valley University, Qena 83523, Egypt;
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