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Roufieda Guerroudj A, Ullah Mughal E, Naeem N, Sadiq A, Al-Fahemi JH, Asghar BH, Boukabcha N, Chouaih A, Ahmed SA. Exploring Pyrimidine-Based azo Dyes: Vibrational spectroscopic Assignments, TD-DFT Investigation, chemical Reactivity, HOMO-LUMO, ELF, LOL and NCI-RDG analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124093. [PMID: 38428162 DOI: 10.1016/j.saa.2024.124093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Theoretical computations of pyrimidine-based azo dyes were performed by the DFT approach using the B3LYP/6 - 31G(d,p) basis set. The molecules were optimized based on the same basis set by calculating the minimum energy. FMOs, DOS and GCRD were computed for kinetic stability and chemical reactivity of the selected compounds. The MEP surface was studied to locate nucleophilic and electrophilic attack zones. The energy gap was carefully studied for pyrimidine-based azo dyes. Vibrational spectroscopy was studied in the most prominent regions with respect to PED assignments. Similarly, the UV-Vis absorption technique was calculated using the TD-DFT approach in different solvent media. The electronic structure of each atom in a molecule was examined via the electron localization function (ELF) and localized orbital locator (LOL). Non-covalent interactions were explored using reduced density gradient analysis. The combination of experimental and theoretical data allowed us to correlate the structural modifications with the observed photophysical properties, facilitating the design of azo dyes with tailored characteristics. This work contributes to the fundamental understanding of azo dyes and offers a foundation for the development of new materials with enhanced photophysical and electronic properties.
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Affiliation(s)
- Ahlam Roufieda Guerroudj
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University of Mostaganem, 27000 Mostaganem, Algeria; Process Engineering Department, Faculty of Technology, Dr. Moulay Tahar University of Saïda, 20000 Saida, Algeria
| | | | - Nafeesa Naeem
- Department of Chemistry, University of Gujrat, Gujrat-50700, Pakistan
| | - Amina Sadiq
- Department of Chemistry, Govt. College Women University, Sialkot-51300, Pakistan
| | - Jabir H Al-Fahemi
- Department of Chemistry, Faculty of Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Basim H Asghar
- Department of Chemistry, Faculty of Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Nourdine Boukabcha
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University of Mostaganem, 27000 Mostaganem, Algeria; Chemistry Department, Faculty of Exact Sciences and Informatic, Hassiba Benbouali University, Chlef, 02000, Algeria
| | - Abdelkader Chouaih
- Laboratory of Technology and Solid Properties (LTPS), Abdelhamid Ibn Badis University of Mostaganem, 27000 Mostaganem, Algeria
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia; Chemistry Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt.
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Perveen M, Noreen L, Waqas M, Mehmood RF, Iqbal J, Manzoor S, Nazir S, Shawky AM, Khera RA. A DFT approach for finding therapeutic potential of graphyne as a nanocarrier in the doxorubicin drug delivery to treat cancer. J Mol Graph Model 2023; 124:108537. [PMID: 37321062 DOI: 10.1016/j.jmgm.2023.108537] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/19/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
In the present work, the drug-loading efficacy of graphyne (GYN) for doxorubicin (DOX) drug is investigated for the first time by using density functional theory (DFT). Doxorubicin drug is effective in the cure of numerous types of cancer including bone cancer, gastric, thyroid, bladder, ovarian, breast, and soft tissue cancer. Doxorubicin drug prevents the cell division process by intercalating in the double-helix of DNA and stopping its replication. The optimized, geometrical, energetic, and excited-state characteristics of graphyne (GYN), doxorubicin drug (DOX), and doxorubicin-graphyne complex (DOX@GYN complex) are calculated to see how effective it is as a carrier. The DOX drug interacted with GYN with an adsorption-energy of -1.57 eV (gas-phase). The interaction of GYN with DOX drug is investigated using NCI (non-covalent interaction) analysis. The findings of this analysis showed that the DOX@GYN complex has weak forces of interaction. Charge transfer from doxorubicin drug to GYN during DOX@GYN complex formation is described by charge-decomposition analysis and HOMO-LUMO analysis. The increased dipole-moment (8.41 D) of the DOX@GYN in contrast with therapeutic agent DOX and GYN indicated that the drug will move easily in the biochemical system. Furthermore, the photo-induced electron-transfer process is explored for excited states, and it reveals that upon interaction, fluorescence-quenching will occur in the complex DOX@GYN. In addition, the influence of the positive and negative charge states on the GYN and DOX@GYN is also considered. Overall, the findings indicated that the GYN could be exploited as an effective drug-transporter for the delivery of doxorubicin drug. Investigators will be inspired to look at another 2D nanomaterials for drug transport applications as a result of this theoretical work.
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Affiliation(s)
- Mehvish Perveen
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Lubna Noreen
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Muhammad Waqas
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Rana Farhat Mehmood
- Department of Chemistry, University of Education, Township, Lahore, 54770, Pakistan
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan.
| | - Sidra Manzoor
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Sidra Nazir
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Rasheed Ahmad Khera
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan.
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Khan MA, Kalsoom S, Ayub AR, Ilyas M, Hassan N, Irshad K, Zeshan M, Arshad S, Zahid MN, El-Fattah AA, Iqbal J. Host-guest coupling to potentially increase the bio-accessibility of 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea by nanocarrier graphyne for brain tumor therapy, a comprehensive quantum mechanics study. J Mol Graph Model 2023; 123:108517. [PMID: 37235904 DOI: 10.1016/j.jmgm.2023.108517] [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: 03/05/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023]
Abstract
This study aimed to explore the potential of Host-Guest coupling with Nanocarrier graphyne (GPH) to enhance the bioavailability of the drug 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea (LUM) for brain tumor therapy. The electronic, geometric, and excited-state properties of GPH, LUM, and the graphyne@1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea-complex (GPH@LUM-complex) were studied using DFT B3LYP/6-31G** level of theory. The results showed that the GPH@LUM-complex was stable with negative adsorption energy (-0.20 eV), and there was good interaction between GPH and LUM in the solvent phase. The weak interaction forces between the two indicated an easy release of the drug at the target site. The Frontier Molecular Orbitals (FMO), Charge Density Analysis (CDA), and Natural Bond Orbital (NBO) analysis supported LUM to GPH charge transfer during complex formation, and the Reduced Density Gradient (RDG) isosurfaces identified steric effects and non-bonded interactions. UV-visible examination showed the potential of the GPH@LUM-complex as a drug carrier with a blue shift of 23 nm wavelength in the electronic spectra. The PET process analysis revealed a fluorescence-quenching process, facilitating systematic drug delivery. The study concluded that GPH had potential as a carrier for delivering LUM, and different 2D nanomaterials could be explored for drug delivery applications. The theoretical study's findings may motivate researchers to investigate the practical applications of GPH@LUM-complex in oncology.
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Affiliation(s)
- Maroof Ahmad Khan
- Key Laboratory of Clusters Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Shehwas Kalsoom
- Department of Chemistry, Concordia College Sahiwal, Pakistan
| | - Ali Raza Ayub
- Key Laboratory of Clusters Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Mubashar Ilyas
- Key Laboratory of Clusters Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Noor Hassan
- Key Laboratory of Clusters Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Kanwal Irshad
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Zeshan
- Department of Pharmaceutical Chemistry, Government College University Faisalabad, Pakistan
| | - Salba Arshad
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Nauman Zahid
- Department of Biology, College of Science, University of Bahrain, Sakhir, P.O. Box 32038, Bahrain
| | - Ahmed Abd El-Fattah
- Department of Chemistry, College of Science, University of Bahrain, Sakhir, P.O. Box 32038, Bahrain; Department of Materials Science, Institute of Graduate Studies and Research, Alexandria University, Alexandria, 21526, Egypt
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan; Department of Chemistry, College of Science, University of Bahrain, Sakhir, P.O. Box 32038, Bahrain.
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Perveen M, Hadia NMA, Noreen A, Mehmood RF, Nasr S, Yahia IS, Khera RA, Iqbal J. Controlled supramolecular interactions for targeted release of Amiodarone drug through Graphyne to treat cardiovascular diseases: An in silico study. J Mol Graph Model 2023; 121:108452. [PMID: 36963305 DOI: 10.1016/j.jmgm.2023.108452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
In the current study, the drug loading ability of graphyne (GY) for the amiodarone (AMD) drug is investigated for the first time. The efficacy of GY as a carrier for amiodarone (a cardiovascular drug) is evaluated by calculating its electronic, energetic, optimized, and excited state properties with help of the density functional theory (DFT). The AMD drug interacted with the GY molecule with an adsorption energy of about -0.19 eV (gas-phase) and -1.92 eV (aqueous phase), suggesting that the AMD@GY complex is stable in water-phase. The HOMO (highest-occupied molecular-orbital) of the AMD@GY complex is concentrated on the AMD drug while the LUMO (lowest-unoccupied molecular-orbital) is centralized on GY with absolute charge separation, indicating charge transfer will occur between AMD and GY. The charge-transfer process is further studied with the aid of charge-decomposition analysis (CDA). The non-covalent interaction analysis (NCI) exposed that non-covalent forces exist between the GY carrier and AMD drug. These non-covalent forces between AMD drug and GY carrier play a significant role in drug unloading at the targeted or diseased site. Likewise, the calculations at excited-state, charge-state (+1 and -1) influence on GY and AMD@GY complex structures, and photo-induced electron transfer analysis (PET) are also studied for the graphyne-based drug-delivery system. According to PET and electron-hole analysis, fluorescence-quenching will occur upon interaction. Overall, it is concluded that graphyne can be exploited as a drug carrier for amiodarone drug delivery. Researchers will be fascinated to look at alternative 2D nanomaterials for drug delivery applications as a result of this theoretical work.
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Affiliation(s)
- Mehvish Perveen
- Department of Chemistry, University of Agriculture, 38000, Faisalabad, Pakistan
| | - N M A Hadia
- Physics Department, College of Science, Jouf University, P.O. Box 2014, Sakaka, Al-Jouf, Saudi Arabia
| | - Asima Noreen
- Department of Chemistry, University of Agriculture, 38000, Faisalabad, Pakistan
| | - Rana Farhat Mehmood
- Department of Chemistry, University of Education, Township, Lahore, 54770, Pakistan
| | - Samia Nasr
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, 61413, P.O. Box 9004, Saudi Arabia; Chemistry Department, Faculty of Science, King Khalid University, Abha, 61413, P.O. Box 9004, Saudi Arabia
| | - I S Yahia
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, 61413, P.O. Box 9004, Saudi Arabia; Laboratory of Nano-Smart Materials for Science and Technology (LNSMST), Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, Saudi Arabia; Center of Medical and Bio-Allied Health Sciences Research (CMBHSR), Ajman University, Ajman, P.O. Box 346, United Arab Emirates
| | - Rasheed Ahmad Khera
- Department of Chemistry, University of Agriculture, 38000, Faisalabad, Pakistan.
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, 38000, Faisalabad, Pakistan.
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Self-assembly for hybrid biomaterial of uridine monophosphate to enhance the optical phenomena. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Louis H, Charlie DE, Amodu IO, Benjamin I, Gber TE, Agwamba EC, Adeyinka AS. Probing the Reactions of Thiourea (CH 4N 2S) with Metals (X = Au, Hf, Hg, Ir, Os, W, Pt, and Re) Anchored on Fullerene Surfaces (C 59X). ACS OMEGA 2022; 7:35118-35135. [PMID: 36211036 PMCID: PMC9535727 DOI: 10.1021/acsomega.2c04044] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/08/2022] [Indexed: 05/21/2023]
Abstract
Upon various investigations conducted in search for a nanosensor material with the best sensing performance, the need to explore these materials cannot be overemphasized as materials associated with best sensing attributes are of vast interest to researchers. Hence, there is a need to investigate the adsorption performances of various metal-doped fullerene surfaces: C59Au, C59Hf, C59Hg, C59Ir, C59Os, C59Pt, C59Re, and C59W on thiourea [SC(NH2)2] molecule using first-principles density functional theory computation. Comparative adsorption study has been carried out on various adsorption models of four functionals, M06-2X, M062X-D3, PBE0-D3, and ωB97XD, and two double-hybrid (DH) functionals, DSDPBEP86 and PBE0DH, as reference at Gen/def2svp/LanL2DZ. The visual study of weak interactions such as quantum theory of atoms in molecule analysis and noncovalent interaction analysis has been invoked to ascertain these results, and hence we arrived at a conclusive scientific report. In all cases, the weak adsorption observed is best described as physisorption phenomena, and CH4N2S@C59Pt complex exhibits better sensing attributes than its studied counterparts in the interactions between thiourea molecule and transition metal-doped fullerene surfaces. Also, in the comparative adsorption study, DH density functionals show better performance in estimating the adsorption energies due to their reduced mean absolute deviation (MAD) and root-mean-square deviation (RMSD) values of (MAD = 1.0305, RMSD = 1.6277) and (MAD = 0.9965, RMSD = 1.6101) in DSDPBEP86 and PBE0DH, respectively.
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Affiliation(s)
- Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Destiny E. Charlie
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Ismail O. Amodu
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Mathematics, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Innocent Benjamin
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Terkumbur E. Gber
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540221, Nigeria
| | - Ernest C. Agwamba
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540221, Nigeria
| | - Adedapo S. Adeyinka
- Department
of Chemical Sciences, University of Johannesburg, Johannesburg 2006, South Africa
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Singh G, Samuchiwal S, Hariprasad P, Sharma S. Melioration of Paddy Straw to produce cellulase-free xylanase and bioactives under Solid State Fermentation and deciphering its impact by Life Cycle Assessment. BIORESOURCE TECHNOLOGY 2022; 360:127493. [PMID: 35777645 DOI: 10.1016/j.biortech.2022.127493] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Aiming towards zero waste management of Paddy straw (PS), the study offers a novel route for production of cellulase-free xylanase, using consortia of Trichoderma spp. under Solid State Fermentation (SSF) of PS valorized using nitrogen rich de-oiled neem cake (NC). Life Cycle Assessment (LCA) for enzyme production, performed using SimaPro software, depicted adverse impacts due to electricity consumption (92.84%) and use of ammonium sulphate salt (6.17%). Nonetheless, employing renewable energy and reducing salt consumption could help minimize these impacts. OHR-LCMS study of the partially purified enzyme revealed the presence of β-xylanase and α-L-Arabinofuranosidase. Enzymatic saccharification of various substrates enhanced the release of reducing sugars (mg/g) from corn cob (137.54 ± 0.96), pine needle (41.43 ± 1), sugarcane bagasse (105.17 ± 0.7), and PS (76.66 ± 1.29), demonstrating its applicability in the biofuel domain. LC-MS, ICMPS, and EDX profiling of the residual spent unravelled the manifestation of bioactives, minerals, and silica, playing an essential role as biopesticide and biofertilizer.
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Affiliation(s)
- Garima Singh
- Centre for Rural Development & Technology, Indian Institute of Technology (IIT), New Delhi 110016, India
| | - Saurabh Samuchiwal
- Centre for Rural Development & Technology, Indian Institute of Technology (IIT), New Delhi 110016, India
| | - P Hariprasad
- Centre for Rural Development & Technology, Indian Institute of Technology (IIT), New Delhi 110016, India
| | - Satyawati Sharma
- Centre for Rural Development & Technology, Indian Institute of Technology (IIT), New Delhi 110016, India.
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Insighting isatin derivatives as potential antiviral agents against NSP3 of COVID-19. CHEMICAL PAPERS 2022; 76:6271-6285. [PMID: 35757111 PMCID: PMC9216297 DOI: 10.1007/s11696-022-02298-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 05/23/2022] [Indexed: 12/18/2022]
Abstract
The world is now facing intolerable damage in all sectors of life because of the deadly COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2. The discovery and development of anti-SARS-CoV-2 drugs have become pragmatic in the time needed to fight against this pandemic. The non-structural protein 3 is essential for the replication of transcriptase complex (RTC) and may be regarded as a possible target against SARS-CoV-2. Here, we have used a comprehensive in silico technique to find potent drug molecules against the NSP3 receptor of SARS-CoV-2. Virtual screening of 150 Isatin derivatives taken from PubChem was performed based on their binding affinity estimated by docking simulations, resulting in the selection of 46 ligands having binding energy greater than -7.1 kcal/mol. Moreover, the molecular interactions of the nine best-docked ligands having a binding energy of ≥ -8.5 kcal/mol were analyzed. The molecular interactions showed that the three ligands (S5, S16, and S42) were stabilized by forming hydrogen bonds and other significant interactions. Molecular dynamic simulations were performed to mimic an in vitro protein-like aqueous environment and to check the stability of the best three ligands and NSP3 complexes in an aqueous environment. The binding energy of the S5, S16, and S42 systems obtained from the molecular mechanics Poisson-Boltzmann surface area also favor the system's stability. The MD and MM/PBSA results explore that S5, S16, and S42 are more stable and can be considered more potent drug candidates against COVID-19 disease. Supplementary Information The online version contains supplementary material available at 10.1007/s11696-022-02298-7.
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